Environmental problems associated with the use of water are inherently complex, involving the interaction of several different systems. Further, there is often limited data on the interaction, because of its location between disciplines. In order to study these problems in a quantitative, policy relevant way, a numerical model is required that integrates the different systems and is tailored to contain the processes important to the interaction. A numerical water resource system model is developed to study the problems associated with the interaction between agriculture and water. The model integrates an econometric model of farmer behaviour with a dynamic model of water flow and solute transport. The Argolid valley in Greece represents an area where severe environmental problems have arisen as a result of the overexploitation of groundwater for agriculture. When applied to the Argolid valley the water resource system model reproduces the evolution of the environmental problems that have arisen. It is then demonstrated that the model can be used to investigate some future scenarios and policy options related to the environmental problems that have developed. The main contribution of this research is to demonstrate that a properly designed numerical model that reproduces the dynamic interaction between human behaviour and the physical environment can enable the exploration of the evolution of environmental problems despite a lack of calibration data. Having achieved this the model can then be used in a policy relevant way to investigate the implications from a range of different, possible policy options.

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Flood inundation phenomena typically occur over reach lengths of 5- 30 km and incorporate a number of complex flow mechanisms. These include a momentum transfer between the main channel and floodplain and turbulent mixing caused by the delivery of water to the floodplain from the channela nd its subsequenrte turn. However, currently available one dimensional schemes applicable at scales appropriate to floodplain inundation processes cannot effectively simulate such processes. This is due to both an incomplete description of the flow physics and a failure to treat floodplain areas in realistic fashion. More complex two and three dimensional models, which have these capabilities, have only been applied over very short reach lengths (c. 0.5 -2 km) and rarely to compound meandering channels. This thesis reports on the further development of a generalized two dimensional, finite element code (RMA-2) to meet this research need. This is achieved via a series of modifications to the numerical model and to the physical representation by finite elements that enable river channel/floodplain flow at the long reach scale to be effectively simulated. Evaluationo f the enhancedR MA-2 schemef ollows a three stages trategy. Firstly, the assumptions underlying the scheme are examined to identify possible inconsistencies. Secondly, tests are undertaken to assess whether the specified physical model has been correctly transferred into computer code. This is achieved via sensitivity analysis, examination of numerical stability issues and investigation of model response to abnormal parameterization. Thirdly, model predictions of flow field information are compared to observed field data in the context of an application of the enhanced model to an 11 km reach of the River Culm, Devon, UK. Results from this evaluation process indicate that the enhanced RMA-2 model is capable of simulating main channel/floodplain momentum transfer and the two dimensionale ffects associatedw ith compoundm eanderingc hannelsa t this scale. Model simulations compare favourably to field data, both for specific cross sections and over the entire mesh. Finally, extension of this core modelling capability is begun via the development of two model application scenarios. These demonstrate the likely utility of the enhanceds chemef or the assessmenotf flood risk and the investigationo f sediment depositionp rocessesin floodplain systems.

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In the course of my duties as a hydrologist with a British regional water authority, I am frequently required to derive riverflow statistics for catchments for which there is little or no measured flow data. Whilst there are many existing methods by which flows may be estimated, my experience has been that the majority of these approaches are unreliable. This thesis describes the development of a suite of alternative, user orientated, high and low flow estimation techniques for application in ungauged catchments. As the derived methods require the cross reference between a large number of figures, these have grouped together as a separate volume, together with appendicies which include all analysed data. However, second copies of selected figures and all summary tables have been included within the main text as an aid to explanation.

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Small temperate lakes are under increasing pressure from a number of anthropogenic sources, including but not limited to: habitat alteration, invasive species, climate change, and pollution. In Gatineau Park, Quebec, Canada small temperate lakes have been demonstrated to be under threat from introduced piscivores, among other potential stressors. Here, I assessed the historical impact of four introduced piscivores on minnow, small fish and total fish species richness for a set of small Gatineau Park lakes. Fish community data were obtained from two previously published studies and a lake survey conducted in the summers of 2006 and 2007. I used a modified Control/Impact study design and repeated measures analysis of variance to test the hypothesis that introduced piscivores negatively affect species richness over time. My results strongly demonstrate that piscivores have had a negative effect on minnow and small fish species richness over time, whereas total fish species richness was unaffected. Assuming that these introduced piscivores pose a risk to the parks small temeprate lakes, I then assessed what lake characteristics best predict piscivore invasion risk. To do this, I estimated invasion risk employing two different analytical approaches for a total of 42 small lakes located in Gatineau Park using current and historical data collected in 1971, 1981, 1991 and 2006. Bootstrapped logistic regression was used to predict historical occurrence, and whether or not a lake was invaded/not invaded over time using predictor variables that included lake anthropogenic, spatial-isolation, and morphometric factors. For both logistic regression analyses, lake area and small fish species richness were found to be excellent predictors of piscivore invasion risk and historical occurrence, while lake spatial-isolation factors were also found to be excellent predictors of piscivore historical occurrence. The bootstrapped models with the most support based on Akaike's Information Criterion corrected for small sample size (AICc) were then used to identify lakes at greatest risk for future invasion. My results support the contention that introducing top predators into novel aquatic environments has detrimental impacts on native fish communities, and that these impacts are not always immediately obvious, but are indeed discernable over time. In conclusion, I make specific recommendations to guide the conservation and management of small temperate lake ecosystems.

Photodegradation rates of methylmercury (MeHg) were measured in water samples from several lakes in the Lake Berthelot region in Quebec in order to investigate the impact of drainage basin logging and associated changes in dissolved organic carbon (DOC) concentrations on MeHg levels in lake water. The lakes were selected on the basis of the amount of logging that had previously taken place in the drainage basin, and on DOC levels which were correspondingly higher in logged lakes due to increased runoff. Lakes DA9 and DF9 had DOC concentrations of 12.3 and 20.9 ppm, respectively and were designated as high DOC for the purposes of this study. Lakes N55 and N70 had DOC concentrations of 6.9 and 6.8 ppm, respectively and were designated as low DOC lakes. Experiments were conducted with both ambient and 2 ppt spiked MeHg levels in the high and low DOC lakes to determine whether the spiked levels reflect photodegradation patterns occurring in nature. The effect of different sized DOC fractions on photodegradation rates were also examined. Upon spiking, the binding of added MeHg reached equilibrium virtually immediately (within minutes) for all size fractions. It was hypothesized that less photodegradation of MeHg would be found in high DOC lakes than in low DOC lakes. In contrast to expected results, no photodegradation was observed in the two lower DOC lakes, but there was photodegradation in the two higher DOC lakes. Hypothesizing that larger size fractions of DOC would result in lower methylmercury (MeHg) photodegradation rates, water samples were fractionated into three DOC size fractions (300 kDa, 30 kDa, and 5 kDa). In the two high DOC lakes in which photodegradation was detected, DOC size fractions had an effect on photodegradation rates, though this effect varied. Average k values (hr-1) for DA9 were -1.25 x 10-1 for the 5 kDa fraction, -1.16 x 10 -1 for the 30 kDa fraction, and -9.21 x 10-2 for the 300 kDa fraction, indicating a decrease in photodegradation rates with larger fractions. For DF9, average k values were -1.69 x 10-1 for the 5 kDa fraction, -6.38 x 10-2 for the 30 kDa fraction, and -1.34 x 10-1 for the 300 kDa fraction, which does not indicate a clear trend in photodegradation rates with respect to DOC size fraction. A comparison of samples from a wetland outflow using ambient MeHg levels demonstrated that 300 kDa DOC fractions showed no photodegradation while 5 kDa DOC showed photodegradation with a k value of -9.12 x 10-2 (hr-1). Overall, watershed logging status was found not to affect MeHg photodegradation rates in the lakes studied. A possible contributor to the variation in photodegradation rates between lakes was postulated to be pH, with H+ ions displacing MeHg from binding sites on DOC and rendering it available for photodegradation. To study the relationship between rates of photodegradation and pH, water samples were adjusted to pH values of approximately 4.5, 6.5, and 7.5 and incubated in sunlight. Rates of photodegradation increased with decreasing pH conditions in all lakes, except for one lake (N55) which also had no detectable photodegradation during the initial field trials. In the remaining three lakes studied, however, lower pH values (4.1-4.6) resulted in greater photodegradation than higher pH values that resulted in little or no photodegradation. It appears that this effect only occurs in lakes with a potential for photodegradation. As results suggested that the size of DOC controls rates of photodegradation, samples were analyzed for the size of DOC and corresponding MeHg content using tangential flow ultrafiltration (TFUF). The efficacy of the TFUF system as a means of both removing microbes as well as fractionating DOC into differing size fractions was evaluated. Results indicated that this is an effective field-portable method. Mass balances for MeHg recovery after filtering large volumes of water were found to be 96% for the 5 kDa filter, 81% for the 30 kDa filter, and 109% for the 300 kDa filter, while flow rates decreased by 26%, 17%, and 50% respectively. Potential artifacts of DOC fractionation using the TFUF were investigated. The amount of DOC passing through the filter was found to decrease with increasing volume of filtrate that passed through the membrane.

<p> An understanding of the spatial and temporal diversity of benthic invertebrates is necessary to understand, manage, and protect freshwater habitats. Benthic invertebrates are important components of aquatic ecosystems and are frequently used in bioassessment and biomonitoring programs. Benthic invertebrates can also play a role in nutrient cycling in lentic environments through bioturbation activities. This dissertation uses a range of techniques and analyses to understand the arrangement of benthic invertebrate diversity in Upper Klamath Lake, Oregon, and several watersheds in northern southern California. </p><p> Upper Klamath Lake (UKL) is a large, shallow, naturally eutrophic lake that has experienced declines in water quality, which has led to annual cyanobacterial blooms of <i>Aphanizomenon flos-aquae</i>. Benthic invertebrates can increase autochthonous nutrient cycling through benthic bioturbation activities. In order to better understand the role that benthic invertebrates play in UKL, I studied the density, taxonomic richness, and species composition of benthic invertebrate assemblages in three geographic regions (north, central, and south) and three habitats (littoral, open-water and trench) across UKL. I also characterized sediment composition and water quality at each collection site and determined which environmental variables correlated with differences in benthic invertebrate composition. This research is located in Chapters 1 and 3 of this dissertation. </p><p> Like benthic invertebrates in UKL, the mayfly <i>Baetis tricaudatus </i> is an abundant and ecologically important organism of freshwater ecosystems. Despite its widespread distribution, <i>B. tricaudatus</i> cannot be consistently and accurately identified and belongs to a species group known to have cryptic species diversity. While previous studies have examined the spatial distribution of this diversity, none have studied the temporal distribution. To better understand the temporal arrangement of diversity at the cytochrome oxidase subunit 1 (CO1) mitochondrial gene region, I collected <i> B. tricaudatus</i> specimens from 3 sites over 4 years and used haplotype networks to visualize diversity. Because my results were different than those from other studies on the same taxon, for my final chapter I analyzed <i> Baetis rhodani</i> group COI sequences from northern and southern California using Bayesian phylogenetic analyses and haplotype networks. This research contributes to our understanding of genetic diversity, which is an important component to biodiversity.</p><p>