The research assessed the potential of developing a selective breeding programme for the UK rainbow trout industry. Levels of genetic variation at 12 microsatellite loci were first compared in seven different commercial strains. The Observed heterozygosity ranged from Ho = 48.1% in a gold rainbow trout strain (GTR) to Ho = 66.4% in a newly derived broodstock population constructed from a number of different sources (GIT). The Expected Heterozygosity (He) was highest in GIM1 (He= 79.5%) and lowest in the GTR strain (He = 56.9%). The Effective number of alleles (Mae) showed that the GIM1, GIM2, GIM3, and GIT strain (5.4; 5.2; 4.8; 4.2) were significantly more variable than the other strains and that GTR strain had the lowest value (2.5). There appears to be substantial genetic variability within the commercial United Kingdom rainbow trout strains surveyed in this study. This appears to be the case despite very different management histories and levels of record keeping. The strains appear to be genetically distinct (based on population genetic analyses), though the reasons for this remain unclear (and possibly unanswerable given the poor records kept by the different companies). The Glenwyllin farm strains (GIM) were chosen to form the base population for the project because of their high genetic variability, disease free status and because the farm produced around 20 million ova per year, so any genetic gains would have a widespread impact. The farm has an early (Strain A) and a late spawning (Strain B) and these were mated in a partial factorial design, 20 females and 20 neomales per strain (A & B) were chosen on the basis of maturity and gamete quality in November 2002 so that each male was crossed to 4 females (2 in the same strain and 2 in the other), a total of 160 families were created. All broodstock were biopsied to enable them to be genotyped. The families were reared separately up to the eyed stage at which point the eggs from each family were divided into three to generate three communal replicate populations. One of these was sent to a fingerling producer (Iwerne Spring) for ongrowing to fingerling size and formed the basis of a commercial production trial at Test Valley Trout farm (TVT) in Hampshire. When the fish reached an average weight of 5 g they were transferred from Iwerne Spring to TVT and 1500 were randomly selected, PIT tagged and biopsied to enable them to be assigned to their family using 11 multiplexed microsatellite loci. Parental assignment was based on exclusion (FAP) but the results were compared with another parental assignment based on likelihood (PAPA). Of the 1500 offspring (OIM) PIT tagged 1242 82.8% could be assigned to a single family utilizing different combinations of more than 6 loci (6 to 11). The growth of the 1500 OIM fish was tracked throughout the grow out period before they were finally harvested and fully processed. The results of OIM strain at the end of the trial period were mean weight of 415.5 g, and a mean length of 314.5 mm. The visual measurement of colour gave a mean flesh colour values of 26.01 on the 20-34 scale (SalmoFan™), and 11.0 with the colotimetry evaluation of colour (a*). The heritability results for the IOM strain were 43 ± 9% for weight, 42 ± 9% for gutted, and 28 ± 8% for length. The heritability estimates for the visual colour variables were 19 ± 7% and when using the colorimeter, the red chromaticity (a*) heritability was 14 ± 6%. Therefore, the heritability results of the IOM strain indicate that there are opportunities of substantial and rapid improvement of the growth rate and flesh colour traits. Also no line effects were observed or indications of non-additive genetic variation. In contrast to these last results, the overall survival of the GIM strain from the time of the physical tagging with PIT until harvest was 52.8%, and survival heritability was extremely low, 3 ± 2%, hardly significant.

Disease has been identified as a major problem in the aquaculture industry for the welfare of the fish stocked as well as for its economic impact. The number of diseases affecting cultured fish has increased significantly during recent years with the emergence of several conditions that have added to the overall impact of disease on the industry. Frequently, a lack of scientific knowledge about these diseases is compounded by an absence of effective treatment and control strategies. This has been the case with rainbow trout gastroenteritis (RTGE), an emerging disease of rainbow trout (Oncorhynchus mykiss Walbaum). This study investigated several aspects related to its aetiology and control. A retrospective survey of UK rainbow trout farmers was undertaken to ascertain the extent and severity of RTGE in the UK as well as to identify RTGE risk factors at the site level. Participants in this study accounted for over 85% of UK rainbow trout production in 2004. It was found that the total number of RTGE-affected sites had risen from 2 in the year 2000 to 7 in 2005. The disease was only reported from sites producing more than 200 tonnes of trout/year for the table market. Analysis of risk factors associated with RTGE at the site level showed that this syndrome was associated with large tonnage and rapid production of rainbow trout for the table market. The data collected during this study enabled the identification of those sites that were most likely to present with RTGE the following year and this information was used to study the epidemiology of RTGE at the unit level. A prospective longitudinal study was undertaken in 12 RTGE-affected UK sites. It described in detail the impact, presentation, current control strategies and spread pattern of RTGE within affected UK sites. The risk factors associated with RTGE presence and severity were also investigated. Data were collected for each productive unit (i.e. cage, pond, raceway or tank) on the mortalities, fish origin, site management and environmental factors. RTGE was identified using a case definition based on gross pathological lesions. Analysis of these data revealed that RTGE behaved in an infectious manner. This conclusion was supported by the presence of a pattern typical of a propagating epidemic within affected units. Also, the risk of an unaffected unit becoming RTGE positive was increased if it had received fish from or was contiguous to a RTGE-affected unit. The presentation also suggested an incubation period of 20-25 days. Risk factor analysis identified management and environmental risk factors for RTGE, including high feed input and stressful events, which could be used to generate a list of control strategies. A study of the histopathological and ultrastructural presentation of RTGE was conducted. The location of segmented filamentous bacteria (SFB) and pathological changes found in affected fish were examined. Pyloric caeca were the digestive organ where SFB were found more frequently and in higher numbers, suggesting that this was the best location to detect SFB in RTGE-affected trout. Scanning and transmission electron microscopy revealed a previously undescribed interaction of SFB with the mucosa of distal intestine and pyloric caeca and this included the presence of attachment sites and SFB engulfment by enterocytes, as previously described in other host species. The SFB were not always adjacent to the pathological changes observed in the digestive tract of RTGE-affected trout. Such changes included cytoskeletal damage and osmotic imbalance of enterocytes, with frequent detachment. These observations suggested that if SFB are indeed the cause of RTGE their pathogenesis must involve the production of extracellular products. Analysis of the gross presentation and blood biochemistry in RTGE-affected fish was used to examine the patho-physiologic mechanisms of RTGE. To enable identification of positive RTGE cases for this study, a case definition was created from the information available on RTGE gross presentation in the literature. This case definition was assessed in a sample including 152 fish cases and 152 fish controls from 11 RTGE-affected UK sites, matched by unit of origin. The analysis of these fish using bacteriology, packed cell volume (PCV) and histopathology revealed that RTGE occurred simultaneously with other parasitic and bacterial diseases in a percentage of fish identified with this case definition. With the information gained after analysing the gross presentation, RTGE-affected fish without concurrent disease were selected for the study of the pathogenesis, which included blood biochemical analyses. These analyses revealed a severe osmotic imbalance, and a reduced albumin/globulin ratio suggesting selective loss of albumin, typical for a protein losing enteropathy. The role of the SFB “Candidatus arthromitus” in the aetiology of RTGE was assessed using a newly developed “C. arthromitus”-specific polymerase chain reaction assay (PCR) in conjunction with histological detection. This technique was applied to eight different groups of trout, including an RTGE-affected group and seven negative control groups. This analysis was conducted on DNA extracted from paraffin wax-embedded tissues as well as fresh intestinal contents. The results revealed the presence of “C. arthromitus” DNA in apparently healthy fish from sites where RTGE had never been reported. Additionally, SFB were observed histologically in two trout from an RTGE-free hatchery. These findings do not permit the exclusion of “C. arthromitus” as the aetiological agent for RTGE, although they suggest that the presence of these organisms in the digestive system of healthy trout is not sufficient to cause clinical disease, and therefore other factors are necessary. In conclusion, this study has used a multidisciplinary approach to the study of RTGE which has generated scientific information related to the epidemiology, pathogenesis and aetiology of this syndrome. The results of this project have suggested priority areas where further work is required, including experimental transmission of RTGE, field assessment of the control strategies proposed and further investigation into the aetiology of RTGE.

I Österdalälven har mängden Siljansöring (Salmo trutta) minskat avsevärt på grund av kraftverk som stoppar fiskens vandringsvägar. För att lyckas med att stärka beståndet krävs en fördjupad kunskap kring fiskens beteendemönster, bland annat rörelser i samband med uppströms lekvandring. Denna studie är ett försök att ge en överblick av den lekmogna Siljansöringens uppströmsvandring i Österdalälven och se om det föreligger några skillnader mellan odlad/vild öring respektive hanar/honor. Genom akustisk telemetri har 18 Siljanöringars rörelser längs en begränsad älvsträcka registrerats under 56 dagar. Analys har gjorts för hitta variationer både rumsligt och tidsmässigt samt mellan odlade/vilda Siljansöringar respektive honor/hanar, likväl som skillnader avseende rörelser, tim- och dygnsaktivitet och benägenhet att söka sig uppströms till det definitiva vandringshindret Spjutmo kraftverk. Siljansöringarna rörde sig mer under dagen jämfört med natt vilket skulle kunna kopplas till påverkan från elproduktion och vattenströmmar som skapas vid Spjutmo kraftverks turbinutlopp och/eller att dagsljuset är en fördel då de använder sig av synintryck för att kunna navigera. Skillnader (dock ej statistiskt säkerställda) kunde urskiljas mellan odlade och vilda fiskar och hanar/honor, såsom exempelvis att vild fisk simmade längre sträckor än odlad. Studier som denna är viktiga för att kunna få en helhetsbild kring livsvillkor och beteendemönster för Siljansöring och därigenom lyckas med framtida förvaltnings- och åtgärdsarbeten. / The number of Siljan trout (Salmo trutta) in the River Österdalälven has declined due to hydropower development. To restore the river information about the behavioural patterns of the trout, such as upstream migration, are needed. The aim of this study is to describe the upstream movements of tagged Siljan trout as well as to identify differences between hatchery-reared and wild trout and between males and females. During 56 days, 18 individuals tagged with acoustic telemetry transmitters were registered in a section of the River Österdalälven. The data were analysed to identify variation in time and space as well as differences between origin (hatchery-reared vs wild trout) and sex. Analyses were also performed on hourly and diel movement patterns and if the fish swam upstream to the first migration barrier, the power station in Spjutmo. Variation in diurnal activity was identified, with higher activity during daytime compared to night, which might be related to power production in relation to currents flowing from turbine outlets and/or the importance of daylight for effective navigation. There were no significant differences identified between hatchery-reared and wild trout, respectively, nor were there any sex-related differences. Information obtained from this study is important to understand the situation for Siljan trout, to help in future management and restoration of this valuable stock of trout.

Many populations of salmonids are threatened by fragmentation and degradation of spawning habitats. Common remedial measures are habitat restoration and stocking of hatchery fish to support degraded wild populations. Many populations of brown trout in Sweden have been extirpated. The restoration plan for the endangered brown trout in Lake Siljan started decades ago and involves releases of hatchery produced trout. A decline of the spawning run of hatchery fish has been observed. In this study, wild and hatchery fish were tagged and monitored using hydroacustic telemetry during May-October, 2018. Movement patterns were studied to detect potential differences between wild and hatchery fish during lake and spawning migration. The results showed a difference of preferred territories between the groups. The wild trout stayed in the northern part of the lake and the hatchery trout were more evenly distributed over the lake, but with a preference for the southern part of the lake. During spawning migration a larger proportion of the wild trout (44 %) moved to potential spawning habitats as compared to hatchery trout (16 %). The wild fish migrated more or less direct to the potential spawning grounds in River Österdal as compared to the hatchery fish, which showed an erratic behavior and preferred to migrate to the tributaries in Lake Siljan. Differences in movement patterns and preferred habitats in the lake can be caused by differences in behavior between the groups. This should motivate more studies of behavior of wild and hatchery trout. The time for spawning and potential spawning habitats are also important to study for future management and restoration of the wild population of brown trout in Lake Siljan. / Många salmonider är idag hotade av habitatfragmentering och brist på lekplatser. För att främja kvarvarande bestånd är vanliga åtgärder habitatrestaurering och utsättning av odlad fisk. Många bestånd av sjövandrande öring i Sverige är idag försvunna. I sjön Siljan har man under årtionden satt ut odlad fisk då den vilda stammen av siljansöringen är starkt hotad. En minskning av återvändande uppströmsvandrande odlad lekfisk har uppmärksammats. Vild och odlad öring märktes med sändare och data samlades in med akustisk telemetri under maj till oktober, 2018. Eventuella skillnader i rörelsemönster mellan fisk av olika ursprung har studerats under tillväxtperiod och lekmigration. Resultatet visade att det finns skillnader i var fiskarna uppehåller sig i sjön beroende på ursprung. Den vilda öringen föredrog den norra delen av Siljan, den odlade var mer spridd i hela sjön men föredrog den södra delen av sjön. Under tid för lekmigration rörde sig en större andel av den vilda fisken (44 %) mot potentiella lekhabitat jämfört med den odlade (16 %). Den vilda fisken var mer fokuserad i sin vandring mot Österdalälven än den odlade som uppvisade ett erratiskt beteende och som i större utsträckning besökte biflöden som mynnar i Siljan. Skillnader i rörelsemönster och placering i sjön kan bero på beteendeskillnader och interaktioner mellan grupperna. Detta borde öka intresset för att studera detta vidare hos den vilda och odlade öringen. Önskvärt är också att öka kunskapen om lekperiod och potentiella lekhabitat för att kunna upprätta ett effektivt åtgärdsprogram som ger ökade möjligheter för en återhämtning av den vilda populationen.

This dissertation describes two different projects. The first is the development of an oral DNA vaccine delivery system for fish. A novel oral DNA vaccine delivery system was developed for Rainbow Trout by combining non-viral vectors (polycationic liposomes or polycationic polymer) to facilitate the DNA vaccine's uptake by cell membranes along with enteric-coated protection of the DNA embedded in microparticles to prevent DNA degradation in the gastrointestinal tract. Spray drying and spray coating bead techniques were employed in the preparation of the DNA vaccine microparticles. The spray drying technique allowed production of spherical shape enteric-coated microparticles with a particle size range of 0.18 to 20 ��m. Larger particle sizes of 40-50 mesh were obtained from the spray-coated bead technique. The resultant DNA vaccine microparticles were granulated with regular fish feed and given to fish to investigate the efficacy of the delivery system in providing protection against IHNV, and to demonstrate the ease of administration in fish. An in vivo fish trial experiment showed improvement in fish survival rate when fish were immunized with larger particle size DNA vaccine microparticles. Further research to find effective vector carriers for the DNA vaccine delivery system and to seek modifications of the delivery system that will still prevent the denaturation of plasmid DNA that will also facilitate membrane uptake of the DNA vaccine is needed in order to develop a safe, effective, and commercially viable vaccine to control the outbreak of IHNV. The second project of the dissertation is prediction of in vitro drug release profiles from a novel matrix tablet spray-coated with a barrier membrane using mathematical and statistical models. Tablets were prepared by direct compression followed by spray coating. The relationship of the amount of hydrophilic materials in the core tablets and barrier thickness on drug release mechanism was investigated using factorial design and regression analysis. Drug release characteristics were influenced and can be controlled by modifying the amount of hydrophilic materials in the core tablet and the barrier thickness. Mathematical equation generated from regression analysis of n-value, lag time, and percent drug release as a function of the amount of hydrophilic material and the amount of coating material applied can now be used as a tool for predicting and optimizing in vitro drug release from matrix tablets spray-coated with a barrier membrane. / Graduation date: 2003

Interest in the subject of fish welfare is continuing to grow, with increasing public awareness and new legislation in the UK. Water quality has long been recognised as being of prime importance for welfare: water provides the fish with oxygen and removes and dilutes potentially toxic waste metabolites. This thesis investigates the interactions between water quality and the welfare of farmed rainbow trout (Oncorhynchus mykiss Walbaum). A literature review was undertaken to identify current recommended water quality limits for the health and welfare of farmed rainbow trout. Contradictions in the literature regarding suggested ‘safe’ water quality limits were also identified, as were deficiencies in some of the methods used to arrive at conclusions for recommended limits. The literature relating to the effects of poor water quality on welfare were also reviewed. The review ends with a discussion about water quality monitoring in the context of on-farm welfare assessment and how the information might be used in such a scheme. A telephone survey of UK rainbow trout farmers was undertaken to ascertain the level of water quality monitoring currently conducted. Participants in this study accounted for over 80% of 2005 UK rainbow trout production. It was established that 54% of farmers monitored dissolved oxygen to some extent and 69% monitored temperature, the most commonly measured water quality parameters and among the most important for health, welfare and growth. Subsequent visits were made to a sample of the participants in the telephone survey to obtain more detailed information of the farming operations, such as frequency of water quality monitoring, retention of production data and slaughter methods. Monitoring water quality will be an integral part of any on-farm welfare assessment scheme, and while measuring some water quality parameters requires specialist equipment, farmers should be able to monitor the essential parameters, dissolved oxygen and temperature. Any on-farm welfare assessment scheme for rainbow trout should incorparate fish-based measures in addition to resource-based parameters in order to provide as complete an overview of trout welfare as possible. An epidemiological study was undertaken to investigate the current status of welfare on UK rainbow trout farms and to identify risk factors for welfare. Forty-four trout farms from throughout the British Isles were visited between July 2005 and April 2007, sampling a total of 3700 fish from 189 different systems. Farms were visited twice, once in winter and once in summer, to account for any seasonal differences in fish physiology and environmental conditions. Data were collected on a range of fish parameters, together with background information on the batch from which the fish originated. Particular emphasis was placed on water quality due to the potential effects this can have on welfare. The water in each system sampled was monitored for 24 hours, with measurements of dissolved oxygen, temperature, pH, specific conductivity and ammonia taken every 15 minutes. A welfare score was developed for each fish using a multifactorial method, combining data on the condition of the fins, the condition of the gills, the stress hormone cortisol, the splenosomatic index and the mortality levels for the population of fish in the system. Using this welfare score and the individual components of the score as response variables, multi-level models were developed using the water quality, system and husbandry data collected. The primary risk factor that was associated with deteriorating welfare was disease. The purpose for which the fish was being farmed was also important, as fish farmed for the table market had on average worse welfare than those farmed for restocking fisheries. Seasonal effects, linked to higher water temperatures in summer, were associated with poorer welfare scores. Aside from seasonal effects, there is not much evidence that poor water quality is a major problem for the welfare of farmed rainbow trout in the UK. While deteriorating water quality certainly has the potential to affect the welfare of farmed rainbow trout, water quality measurements were within recommended ranges for the majority of farms visited. The results of this epidemiological study suggest that factors other than water quality may have a greater impact on trout welfare, such as exposure to diseases and production differences between farming for the table and restocking markets.

Species of Argulus are macro-, ecto-parasites known to infect a wide variety of fish, but in the UK mainly cause problems in rainbow (Oncorhynchus mykiss) and brown trout (Salmo trutta). Argulus foliaceus is estimated to have caused problems in over 25% of stillwater trout fisheries in the UK. While A. foliaceus does not usually cause high levels of mortality, the parasite affects fish welfare, and also makes fish harder to catch due to morbidity and reduced appetite. This can cause severe economic problems for the fishery, resulting in reduced angler attendance due to poor capture rates and the reduced aesthetic appearance of fish; in the worst-case scenario this can result in the closure of the fishery. Current methods of control include chemical treatment with chemotherapeutant emamectin benzoate (Slice), physical intervention with egg-laying boards which are removed periodically and cleaned in order to reduce the number of parasites hatching into the environment, and the complete draining and liming of the lake to remove all free-living and egg stages of the parasite. While these treatments have all been shown to reduce parasite numbers, none are known to have resulted in permament eradication of the parasite. There is evidence to suggest that A. foliaceus will eventually develop resistance to Slice - the only currently available chemical treatment against the infection - and egg-laying boards and the draining and liming of the lake are both time- and labour-intensive. Previous studies have shown that slow fish turnover is a risk factor with respect to A. foliaceus infections, and with a wide variety of stocking practices occurring in the UK one of the first aims of this project was to determine their impact on the host-parasite dynamics. Mathematical models provide a cost-effective way of examining the impact of such practices, and after a literature review (chapter one), in chapter two a three-compartment mathematical model was adapted for use in the A. foliaceus-trout system. Four generalised stocking methods were then incorporated and analysed, and a minimum threshold host density was found to be necessary to sustain the parasite. Including a function which reduced the capture rate as the parasite burden increased allowed the parasite to survive at a lower host density, as susceptible fish were removed from the water at a slower rate, and attached parasites also remained in the water for longer. This resulted in hysteresis in the model, as the invasion threshold for the parasite remained the same, but once established the parasite became harder to eradicate, requiring significant reductions in the host density. In chapter three the model was further developed in order to improve its biological real- ism. Several features were added and these included: natural host mortalities, a separate compartment for the parasite egg population, and parasite survival after the natural or parasite-induced mortality of its host. In chapter four seasonality was added by incorporating temperature-dependent egg-laying rates and an over-wintering period during which the parasite was unable to reproduce. The model was then fit to the available data, and estimates for the rate of parasite-induced host mortalities and the parasite’s rate of attachment to a host were found. In chapter five we returned to stocking methods, this time looking at the frequency and timing of stocking events and the impact of imposing a rod limit (whereby anglers are only permitted to capture four fish per visit); it was concluded that while current guidelines suggest that very frequent trickle stocking is recommended when dealing with Argulus spp. infections, monthly stocking does not appear to worsen the infection, and if the fish capture rate is high then less-frequent stocking may also be permissable - particularly if stocking occurs towards the end of the year when the parasite is no longer active. This practice may, however, be detrimental to the fishery due to low fish densities in the summer months. In chapter six treatment with Slice was included in the model, and it was demonstrated that with constant treatment, and in the absence of reservoir hosts and a withdrawal period from the drug prior to stocking treated fish into the fishery, the parasite was eradicated. Under current veterinary cascade guidelines, however, trout are required to undergo a withdrawal period of 500 degree days prior to being made available for human consumption. When this was included in the model the drug still decreased parasite abundance, but did not eradicate it - this is in agreement with results reported by communications with fishery managers currently treating fish with Slice. A reduction in the withdrawal period of 25% was shown to further decrease parasite abundance, but still did not result in parasite extinction. As constant treatment with Slice is not advisable due to the potential for resistance build-up, we then sought to find time at which to apply a single treatment of Slice, and found that this was in August when the temperature was highest and the parasite was reproducing and attaching to hosts quickly. Egg-laying boards were also incorporated into the model and similarly to findings by Fenton et al. [11] the success of this treatment was mostly dependent on the proportion of eggs being laid on the boards (as opposed to natural substrates). In contrast with the A. coregoni system, however, the boards would have to be cleaned and replaced more frequently that once per year, as several cohorts of A. foliaceus emerge during a single year.

Abstract My main objectives in this thesis were to explore general patterns and mechanisms driving salmonid invasions globally and, more specifically, to examine the invasion dynamics and impacts of the North American brook trout in North European stream systems. Non-native salmonids have often spread extensively and caused many harmful impacts on their native counterparts. Among the three globally introduced salmonids, the European brown trout appeared as the 'worst' alien species (strongest impact on native fish), followed by the North American rainbow trout and brook trout. Brook trout, which is widely established in European streams, was found to be a non-aggressive species. Moreover, the growth of brown trout was unaffected by brook trout, indicating negligible interspecific interactions between the two species. Habitat niche segregation between brook trout and brown trout was evident, with brook trout occupying mainly low-velocity pool habitats, whereas brown trout resided in fast-flowing riffles. At the river-wide scale, brook trout occurred mainly in small, slightly acid headwater streams, whereas brown trout was found primarily in larger downstream river sections. Evidently, North European streams with a very low number of native fish species offer underutilized niche space for tolerant headwater specialists such as brook trout. However, the habitat niche filled by brook trout was not completely vacant, as brown trout co-occurred with brook trout in numerous small and mid-sized (3–16 m wide) streams. In these streams, brown trout reproduction was negligible presumably related to the presence of brook trout. Brook trout had also increased in density relative to brown trout during the 10-yr study period (1994 vs. 2004). Moreover, the growth rate and population densities of brook trout were high and the species had spread extensively towards the upmost headwater streams during the 10-yr study period. Thus, harmful effects on the native brown trout by brook trout are likely to occur in the core habitat of the invader, i.e. headwater streams, leaving populations of the native species unaffected elsewhere. Due to the high conservation value of the potentially impacted populations of brown trout, I strongly caution against further stocking of brook trout in European watersheds.

No description available.

Riverine physical habitats and habitat utilization by fish have often been studied independently. Varying flows modify habitat composition and connectivity within a stream but its influence on habitat use is not well understood. This study examined brown trout (Salmo trutta) and bullhead (Cottus gobio) utilization of physical habitats that vary with flow in terms of size and type, persistence or duration, and frequency of change from one state to another, by comparing groundwater-dominated sites on the River Tern (Shropshire) with surface runoff-dominated lowland, riffle-pool sites on the Dowles Brook (Worcestershire). Mesohabitat surveys carried out at two-month intervals on a groundwater-dominated stream and on a surface runoff-influenced stream showed differences in habitat composition and diversity between the two types of rivers. The temporal variability in mesohabitat composition was also shown to differ between the two flow regime types. In the groundwater-influenced stream, mesohabitat composition hardly varied between flows whereas in the flashy stream it varied to a great extent with discharge. Habitat suitability curves for brown trout and bullhead were constructed to predict the potential location of the fish according to flow. The resulting prediction maps were tested in the field during fish surveys using direct underwater observation (snorkelling). Under the groundwater-influenced flow regime brown trout displayed a constant pattern of mesohabitat use over flows. Mesohabitats with non-varying characteristics over flows and with permanent features such as large woody debris, macrophytes or any feature providing shelter and food were favoured. Biological processes, such as hierarchy, life cycle and life stage appeared to play a key role in determining fish habitat use and to a greater extent than physical processes in these streams. Bullhead observations in the flashy river showed that mesohabitat use varied with flow but that some mesohabitats were always favoured in the stream. Pools and glides were the most commonly used mesohabitat, due to their stability over flows and their role as shelter from harsh hydraulic conditions and as food retention zones. The presence of cobbles was also found to be determinant in bullhead choice of habitat. In this flashy environment, physical processes such as flow and depth and velocity conditions appeared to be a more decisive factor in bullhead strategy of habitat use than biological processes. This research shows that: 1. Though differences in habitat use strategies between the two flow regimes can in part be attributed to differing ecology between the species, flow variability affects fish behaviour. 2. A stable flow regime allows biological processes to be the main driving force in determining fishbehaviour and location. A highly variable environment requires fish to develop behaviour strategies in response to variations in hydraulic conditions, such as depth and velocity, which constitute the key factor in determining fish location.