Thesis (MEng)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: The Swartvlei estuary and lake system is situated on the southern coast of the Western Cape Province of South Africa and forms part of the core conservation area of the Wilderness National Park. The Swartvlei system comprises two interlinked water bodies, namely Swartvlei Lake and Swartvlei estuary. SANParks have been monitoring this estuary closely over the past two decades, due to its importance to the ecology and to tourism. There are also low-lying properties on the perimeter of the Swartvlei estuary which run the risk of occasional flooding. Two of the major monitoring issues in this estuary system are the water level required for successful mouth breaching, and the influence of the water level on the low-lying properties. This study presents a preliminary analysis of the sediment budget across the Swartvlei estuary mouth. The objective of this study was to identify the various sediment contributory factors and to estimate the quantities that each individually contributed towards the defined sediment budget. / AFRIKAANSE OPSOMMING: Die Swartvlei meer en see monding is geleë aan die kaapse suidkus van Suid- Afrika. Dit vorm deel van die kern bewarings area van die Wilderness Nationale Park. Die Swartvlei sisteem bestaan uit twee verbinde, kern dele nl: Swartvlei meer en estuarium. Vir die afgelope twee dekades is hierdie area onder die noue toesig van SANParke as gevolg van die belangrikheid van die area met betrekking tot toerisme en ekologie. Daar is ook menigde laag liggende eiendomme aan die oewers, wat baie sensitief is vir watervlak stygings. Die optimum water vlakke benodig vir die uitskuring van die gety monding het ook implikasies vir die laag liggende eiendome en vereis noukeurige monitering. ‘n Voorlopige analise van die sediment begroting rondom die gety monding word deur hierdie studie voorgelê.

[Truncated abstract] The expansion of human populations in coastal land margins has resulted in major modifcations to estuarine ecosystems. The use of numerical models as predictive tools for assessing remediation strategies is increasing. However, parameterisation of physical processes, developed mainly through field investigations, is necessary for these models to be reliable and effective management tools. The physical processes in micro–tidal diurnal tidal systems are relatively unknown and the current study examines field measurements obtained from the upper Swan River estuary (Western Australia), a diurnal, partially mixed system during the summer when the freshwater discharge is negligible. The aims of the study were to characterise, temporally and spatially, the dominant physical processes and associated sediment resuspension. Variability at three dominant time-scales were examined: 1) sub–tidal oscillations (∼5 to 10 days) resulting from local and remote forcing; 2) tidal (∼ 24 hours) due to astronomical forcing; and 3) intra-tidal (∼2 to 3 hours) resulting from the interaction between tidal constituents. Circulation in estuaries is widely accepted in the literature to be dominated, in varying proportions, by tidal range, freshwater discharge and gravitational circulation. In the upper Swan River estuary sub–tidal oscillations were responsible for the largest upstream displacement of the salt wedge in the absence of freshwater discharge. Moreover, these sub–tidal fluctuations in water level modified the ‘classic’ estuarine circulation. The dynamics of diurnal tides are largely controlled by the tropic month, which oscillates at a slightly different period to the lunar month, resulting in the spring–neap tidal cycle to be sometimes different from syzygy. The phase lag between the diurnal (O1 + K1) and semi-diurnal (M2 + S2) constituents, at the seasonal time scale cause the maximum tidal range to be near the solstice. Over a 24–hour tidal cycle this phase lag is manifested as an intra–tidal oscillation that occurs on the flood tide. Turbidity events that last ∼1 to 2 hours occur during the intra–tidal oscillation, but are not related to maximum shear stress predicted from the mean flow characteristics. The increases in turbidity during the intra–tidal oscillation is, however, correlated with the near–bed Reynolds fluxes. During the intra–tidal oscillation advection opposes the estuarine circulation in the near–bed region, promoting vertical shear that results in destratifcation of the water column. The turbulent mixing generated at the interface and in the near–bed region coincide with resuspension events. Similar turbidity data have often been disregarded and documented as being ‘spikes’ based on the premise that the mean flow was below a critical level to resuspend sediment. Resuspension events were not simply related to mean processes and may be controlled by turbulent instabilities generated when tidal currents reverse during an intra-tidal oscillation

Le modèle input-output régional environnementalisé développé dans la thèse de M. Cordier suggère qu’il serait possible de restaurer 25% des surfaces naturelles de nourriceries de poissons détruites dans l’estuaire de la Seine entre 1834 et 2004. Le modèle suggère que la mesure de restauration pourrait augmenter de 15% à 23% la biomasse de soles produite dans l’estuaire par rapport à une situation sans mesure. Quant à l’effet des coûts de restauration sur les agrégats macroéconomiques (PIB, emploi, etc.), il génère une diminution qui ne dépasse pas 0,5% par rapport à une situation sans mesure. Le modèle montre cependant que trois secteurs sont particulièrement touchés par la mesure, leur bénéfice étant considérablement réduit. Cela indique le compromis à réaliser entre les objectifs écologiques à long terme et les objectifs économiques sectoriels à court terme. La quantification des compromis par le modèle constitue un atout utile aux processus de décision participatifs multicritère / The regional green input-output model developed in Mateo Cordier's PhD shows that it seems possible to restore 25% of the natural areas of fish nurseries destroyed in the Seine estuary between 1834 and 2004. The model suggests that the restoration measure could increase between 15% and 23% the biomass of sole generated by the estuary compared to a situation without measure. Regarding the impact of restoration costs on macro-economic indicators (GDP, employment, etc.), it generates a decrease that does not exceed 0,5% compared to a situation without measure. However, the model shows that three sectors are particularly impacted by the measure. Their benefits are considerably reduced. This shows the trade-off that occurs between ecological targets on the long run and economic targets on the short run. The quantification of such trade-offs in the model is particularly useful to public participation in decision-making. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

La matière organique dissoute (MOD) est constituée d’un mélange hétérogène et complexe de molécules. Elle intervient dans de nombreux processus physiques, biologiques et chimiques dans les milieux aquatiques, et notamment dans les grands cycles biogéochimiques ou le transport et la biodisponibilité des contaminants.Ainsi un des enjeux actuels de nombreux domaines de recherche (chimie, écologie, océanographie) est de mieux comprendre et caractériser la MOD dans l’environnement. Dans ce contexte-là, l’objectif de ces travaux a été le développement d’une méthodologie analytique pour l’analyse et la séparation, en fonction de la taille, par fractionnement par couplage flux-force avec flux asymétrique (AF4) de la MOD. Le développement a principalement porté sur la phase mobile, le flux croisé, le temps de focus et l’utilisation d’étalons organiques proches de la MOD, permettant de calculer sa masse moléculaire moyenne.Cette méthode optimisée, couplée à un détecteur UV/Vis, équipée d’une membrane de 1kDa, d’un espaceur de 490μm et d’une phase mobile de 5mM en tampon phosphate a permis l’étude de la dynamique de la MOD.L’application de cette méthode couplée aux techniques de spectroscopie optique (absorbance et fluorescence) a permis l’étude de la MOD dans les estuaires de Seine et de Gironde mettant en avant les effets de la marée et des saisons sur la taille et le type de MOD.De plus, différentes approches statistiques ont été développées afin de mieux appréhender les multiples variables (analytiques ou environnementales) et notamment les modèles de régression linéaire ou les cartes auto-organisatrices de Kohonen. / Dissolved organic matter (DOM) is a heterogeneous and complex mixture of molecules. It is involved in many physical, biological and chemical processes in aquatic ecosystems, especially in the major biogeochemical cycles or transport and bioavailability of contaminants.Thus one of the current issues in many areas of research (chemistry, ecology, oceanography) is to better understand and characterize DOM in the environment. In this context, the aim of this work was the development of an analytical methodology for DOM analysis and separation, depending on its size, by asymmetrical flow field-flow fractionation (AF4). The development focused on the mobile phase, the cross-flow, the focus time and the use of organic macromolecules standards close to DOM, in order to calculate its molecular weight.This optimized method, coupled with a UV/Vis detector, equipped with a 1kDa membrane, a 490μm spacer and a mobile phase of 5 mM phosphate buffer allowed us to study the MOD dynamics in estuarine environments.The application of this method coupled to optical spectroscopy techniques (absorbance and fluorescence) permitted the study of MOD in the Seine and Gironde estuaries and to highlight the tidal and the seasonal effects on the size and type of DOM.Furthermore, different statistical approaches have been developed to better understand the multiple variables (analytical or environmental), especially linear regression models or self-organizing maps (Kohonen).

Over the last decades, there has been considerable attention in the accurate mathematical modeling and numerical simulations of free surface wave propagation in near-shore environments. A physical correct description of the large scale phenomena, which take place in the shallow water region, must account for strong nonlinear and dispersive effects, along with the interaction with complex topographies. First, a study on the behavior in nonlinear regime of different Boussinesq-type models is proposed, showing the advantage of using fully-nonlinear models with respect to weakly-nonlinear and weakly dispersive models (commonly employed). Secondly, a new flexible strategy for solving the fully-nonlinear and weakly-dispersive Green-Naghdi equations is presented, which allows to enhance an existing shallow water code by simply adding an algebraic term to the momentum balance and is particularly adapted for the use of hybrid techniques for wave breaking. Moreover, the first discretization of the Green-Naghdi equations on unstructured meshes is proposed via hybrid finite volume/ finite element schemes. Finally, the models and the methods developed in the thesis are deployed to study the physical problem of bore formation in convergent alluvial estuary, providing the first characterization of natural estuaries in terms of bore inception. / Ces dernières décennies, une attention particulière a été portée sur la modélisation mathématique et la simulation numérique de la propagation de vagues en environnements côtiers. Une description physiquement correcte des phénomènes à grande échelle, qui apparaissent dans les régions d'eau peu profonde, doit prendre en compte de forts effets non-linéaires et dispersifs, ainsi que l'interaction avec des bathymétries complexes. Dans un premier temps, une étude du comportement en régime non linéaire de différents modèles de type Boussinesq est proposée, démontrant l'avantage d'utiliser des modèles fortement non-linéaires par rapport à des modèles faiblement non-linéaires et faiblement dispersifs (couramment utilisés). Ensuite, une nouvelle approche flexible pour résoudre les équations fortement non-linéaires et faiblement dispersives de Green-Naghdi est présentée. Cette stratégie permet d'améliorer un code "shallow water" existant par le simple ajout d'un terme algébrique dans l'équation du moment et est particulièrement adapté à l'utilisation de techniques hybrides pour le déferlement des vagues. De plus, la première discrétisation des équations de Green-Naghdi sur maillage non structuré est proposée via des schémas hybrides Volume Fini/Élément Fini. Finalement, les modèles et méthodes développés dans la thèse sont appliqués à l'étude du problème physique de la formation du mascaret dans des estuaires convergents et alluviaux. Cela a amené à la première caractérisation d'estuaire naturel en terme d'apparition de mascaret.

The spotted grunter (Pomadasys commersonnii) is an important, estuarine-dependent, fishery species in southern Africa. Since estuaries are essential habitats in the life history of this species, the quantification of area use patterns and movements is important for fisheries management. In this study, acoustic telemetry was used to investigate movements, use of habitat and home range dynamics of spotted grunter in the small intermittently open East Kleinemonde Estuary on the Eastern Cape coast of South Africa. Nine spotted grunter (range: 326-489mm TL) were surgically equipped with uniquely coded acoustic transmitters. Positional fixes were obtained by manual tracking tagged individuals on six days and six nights during five tracking sessions from March to November 2004. In addition, five stationary data-logging receivers, moored at specific locations from the mouth to the top of the estuary provided additional long-term monitoring. Kernel home ranges (95% UD) varied in size (26 296-165 321m²) but were all located in a common high use area situated between 300-1 300m from the estuary mouth, which coincided with the highest abundance of prey items. There was no significant variation in home range size [C² (N = 9, df = 4) = 4.18; p = 0.38] between the temporally segregated tracking sessions (over nine months). The persistence of these home range estimates were confirmed by the long-term data-logging receivers. There was no significant diel variation in home range size [F(4, 64) = 0.05, p = 0.99] or core area size [F(4, 64) = 1.40, p = 0.25]. Fish length showed negative, although not significant, relationships between home range size (p = 0.225); number of home range areas (p = 0.065); core area size (p = 0.512) and home range length (p = 0.320). Use of habitat and home range dynamics of spotted grunter in the East Kleinemonde Estuary were consistent over the nine month study period, and they appeared to be influenced more by biotic than abiotic factors. However, when the mouth opened at the end of the study, most tagged fish vacated their home ranges and emigrated to sea.

The spatial and temporal patterns in selected components of the ichthyofauna and piscivorous avifauna in the small temporarily open/closed Riet River Estuary located on the eastern seaboard of southern Africa was investigated monthly over the period August 2005 to July 2006. The ichthyofauna within the littoral zone of the estuary was sampled using a 5 m seine net (8 stations) while a 30 m seine net (4 stations) was employed to sample the fish in the channel. Bird counts were made along repeat transects along the length of the estuary. Total ichthyofaunal abundances and biomass ranged between 1.60 and 8.67 individuals m⁻² and 0.45 to 21.76 g wwt m⁻² within the littoral zone, and between 0.08 and 0.44 individuals m⁻² and 0.58 and 36.52 g wwt m⁻² in the channel of the estuary. The highest values were generally recorded during the summer months. Results of the numerical analysis indicated that the breaching events recorded over the study period did not lead to a common trend in the ichthyofaunal community. In the absence of a link to the marine environment, the ichthyofaunal community in the littoral zone was numerically dominated by the estuarine resident species, Gilchristella aestuaria and to a lesser extent by Glossogobius callidus, which collectively accounted for ca. 54% of the total ichthyofauna sampled. The establishment of a link to the marine environment coincided with increased numbers of marine breeding species including Atherina breviceps and Rhabdosargus holubi to total fish counts within the estuary. Hierarchical cluster analysis did not identify any spatial patterns in the community structure of the ichthyofauna in the littoral zone or channel zone of the estuary, which could likely be linked to the absence of any distinct horizontal patterns in salinity and temperature within the system. A total of thirteen piscivorous bird species was recorded over the study period. Of the recorded species, six species were wading piscivores, four species were aerial divers and the remaining three species were pursuit swimmers. There were no significant correlations between the estimates of the ichthyofaunal abundance and biomass and bird numbers evident during the study (P> 0.05 in both cases). The Reed Cormorant (Phalacrocorax africanus) was the dominant species throughout the study, with a mean of 8.25 (SD ± 7.90) individuals per count. Mean values of the Pied Kingfisher (Ceryle rudis) and Giant Kingfisher (Megaceryle maximus) were 3.42 (SD ± 1.20) and 1.17 (SD ± 0.60) individuals per count, respectively. The remaining species revealed mean values < 0.5 individuals per count. The highest bird numbers were recorded in winter reflecting the migration of large numbers of the Reed Cormorant into the system. Breaching events were associated with a decrease in total bird numbers, which was most likely due to loss of potential foraging habitat (littoral zone) for waders resulting from reduced water levels. Monthly food consumption by all piscivorous birds revealed large temporal variability, ranging from 26.35 to 140.58 kg per month. The observed variability could be linked to mouth phase and bird numbers.

The spatio-temporal patterns in concentrations of selected metals within the sediment (Cd, Co, Cu, Fe, Pb, Ni and Zn) and water (Cd and Pb) of three permanently open estuaries (Kariega, Kowie, Great Fish) and six temporary open-closed estuaries (Mpekweni, East Kleinemonde, West Kleinemonde, Riet, Kasouga, Boknes) were investigated. The concentrations of metals were influenced by size composition and total organic content of the sediments. Enrichment factors (EFs), using Fe as a reference element, and baseline linear regression models for metals vs. Fe were calculated to assess the extent of metal enrichment in the sediments. The mean concentrations of metals in the sediments(mg·kg⁻¹) showed ranges of 0.28 – 2.31 for Cd, 1.26 – 6.24 Co, 0.69 – 6.93 for Cu, 2119 – 14912 for Fe, 2.29 –14.01 for Ni, 4.81 – 22.20 for Pb and 5.77 – 21.75 for Zn. Mean normalized enrichment factors ranged between 0.75 – 6.19 for Cd, 0.53 – 2.71 for Co, 0.22 – 0.84 for Cu, 0.30 – 1.87 for Ni, 0.99 – 3.17 for Pb and 0.14 – 0.98 for Zn. All nine estuaries had average enrichment factors of greater than 1 for Cd. In general there was no enrichment of Cu and Zn in the sediments of any of the estuaries included in this study (EFs < 1). The Kariega, East Kleinemonde, West Kleinemonde, Riet and Great Fish Estuaries showed some degree of enrichment for Co (1 < EF < 4), Ni (1 < EF < 2) and Pb (1 < EF < 4), while the Mpekweni, Kasouga, Boknes and Kowie Estuaries were unenriched with these metals (EF < 1). Enrichment factors for Cd, Co and Pb typically followed the development gradient along the estuaries, suggesting anthropogenic enrichment. The concentrations of Cd and Pb in the water of the nine estuaries were also determined. The average concentrations of Cd and Pb in the water (μg·ℓ⁻¹) ranged between 0.05 – 3.32 and 0.75 – 34.13 respectively. On average the concentrations of Cd and Pb in the water of all the estuaries were below the South African recommended water quality guidelines for coastal marine waters. Variations in metal concentrations associated with changes in hydrology (wet vs. dry season) were determined in the water and sediment of the Kariega, East Kleinemonde and Riet Estuaries. Cobalt, Pb and Ni enrichment in the Kariega Estuary sediment was significantly higher during the dry season, and the mean concentrations of Pb and Cd in the water column were 19-fold and 66-fold higher in the dry season. The elevated concentration of metals during the dry season could be related to accumulation of diffuse pollution from human activities within the catchment area. Conversely, inflow of fresh water into the estuary had the net effect of reducing the concentration and enrichment of these metals within the Kariega Estuary due to scouring and outflow of estuarine water and sediment into the marine environment. The temporal variations in metal concentrations and enrichment factors were less pronounced in the temporary open-closed estuaries than the permanently open Kariega Estuary. The observed trend can probably be related to the low anthropogenic impact within the catchment areas of these systems, and the relatively smaller size of the catchments. Significant spatial variations existed in metal enrichment in the sediment of both the East Kleinemonde and Riet estuaries, with the highest degrees of enrichment occurring in the sediments from the marine environment and lower reaches.

Coastal transition zones form important interlinking regions where marine ecosystems, rivers and estuarine environments significantly influence each other. Coastal rocky shores are key habitats that sustain a variety of primary producers and invertebrates and due to the dynamic nature of coastal ecosystems, suspension-feeders on rocky shores can be influenced by an array of autochthonous and allochthonous food sources. Fatty acid and stable isotope trophic markers were employed to distinguish between regional and temporal changes in the potential food sources to rocky shore suspension-feeders in the Eastern Cape Province of South Africa. The primary aim was to assess the spatial and temporal influences of contrasting river flows on the available food sources to three indigenous coastal suspensionfeeders, namely the volcano barnacle Tetraclita serrata, brown mussel Perna perna and tubebuilding polychaete Gunnarea capensis. This was done by examining the intra- and interspecific changes in the fatty acid and stable isotope signatures of the barnacles, mussels and polychaetes in the adjacent marine environment of a freshwater-restricted (Kariega) and freshwater-dominated (Great Fish) estuary during austral summer and winter. Multivariate and Kruskal-Wallis analyses of variance on the fatty acid and isotopic signatures, respectively, identified significant regional changes in the barnacles and mussels, while only stable isotopes distinguished between the Kariega and Great Fish polychaetes (P < 0.05). In addition, significant temporal changes were observed in consumer fatty acids and isotope values in both regions (P < 0.05). Bacterial sources, detritus and phytoplankton assemblages, which are influenced by hydrology and vegetation, differed between regions and were mainly responsible for the regional and temporal separations. Principal component analyses on the consumer fatty acid signatures distinguished between animals situated upstream (i.e. north) and downstream (i.e. south) of the Kariega Estuary mouth in summer. The north/south separation was mainly due to greater contributions of diatoms to northernlocated animals and dinoflagellates and detritus to southern-located consumers. In addition, the south-flowing Agulhas Current on the eastern shores of southern Africa appeared to influence the north/south separation in the Kariega region, as water leaving the estuary was probably entrained into the south-easterly flowing currents, thereby depositing estuarinederived detritus to southern populations. In general, diatoms and detritus were essential food sources to the filter-feeders in summer, and flagellates, diatoms, zooplankton and detritus were important in winter. Coastal macroalgae was a key food source in the Kariega and Great Fish regions during both seasons. Consistently large levels of diatom markers (16:1n-7 and 20:5n-3) and dinoflagellate markers (22:6n-3) in consumer tissues in the Kariega and Great Fish regions identified that phytoplankton was their dominant food source. The barnacles, mussels and polychaetes had similar fatty acid markers and a fairly narrow δ¹³C range (-16.5 to -14.4 ‰), suggesting that they probably consumed similar food. Carbon isotope analyses, however, separated the suspension-feeders into slightly depleted (barnacles; -16.5 to -16.1 ‰), intermediate (mussels; -15.8 to -15.0 ‰) and enriched (polychaetes; -15.0 to -14.4 ‰) consumers, but did not provide conclusive evidence of their preferences for specific phytoplankton. Conversely, fatty acid analyses highlighted that barnacles and mussels had greater proportions of dinoflagellate markers (22:6n-3; 7.0-15.3 % TFA), while polychaetes had larger diatom levels (20:5n-3; 15.1-22.2 % TFA). In addition, all three species had consistently large contributions from bacterial fatty acids (15:0, i-16:0, 17:0 and i-18:0; 4.2-13.6 % TFA) in summer and winter, and large proportions of saturated fatty acids (33.3-53.1 % TFA) including those with 14 to 18 carbons, indicating that bacterial and detritus food sources played an important role in their diets. Barnacles had small levels of terrestrial markers (18:2n-6 and 18:3n-3; <2.5 % TFA) and demonstrated increased omnivorous feeding compared with the other suspension-feeders [increased levels of 20:1n-11 and 20:1n-9, higher 18:1n-9/18:1n-7 ratios at ~2.1, enriched δ¹⁵N values at ~10.6 ‰; zooplankton (potentially including microzooplankton, larvae and protists) contribution of up to 61 % of the diet]. Mussels contained significant proportions of the terrestrial markers (18:2n-6 and 18:3n-3; >2.5 % TFA) and exhibited intermediate omnivory (intermediate levels of 20:1n-11 and 20:1n-9, intermediate 18:1n-9/18:1n-7 ratios at ~1.3, less enriched δ¹⁵N values at ~7.9 ‰; zooplankton contribution of 10-15 % of the diet). The more depleted nitrogen signatures in the mussels relative to the barnacles and polychaetes possibly illustrated a stronger preference for autotrophic food. Polychaetes mainly consumed plant food sources (i.e. microalgae, macroalgae and detritus; high levels of i-18:0, 18:1n-9, 18:4n-3 and 20:5n-3) and displayed little omnivory (low levels of 20:1n-11 and 20:1n-9, low 18:1n-9/18:1n-7 ratios at ~0.4, intermediate δ¹⁵N values at ~9.1 ‰; zooplankton contribution of <10 % of the diet). The barnacles, mussels and polychaetes are all suspension-feeders, originally presumed to consume the same food sources. The variations observed among the species, therefore, may result from differences in the proportional contributions of the various food sources to their diets as well as distinctions in metabolism. The distinct changes in the fatty acid and stable isotope signatures in all three filter-feeders in the Kariega and Great Fish regions are likely influenced by the diversity in regional vegetation and hydrology in the different systems, combined with interspecific differences in resource partitioning among the species.

The aims of this study were to determine the potential use of biomarkers at multiple levels of biological organisation together with a fish community bioindicator to assess the estuarine health status of three temporarily open/closed estuaries. The estuaries investigated were the East Kleinemonde (EK), Old Woman's (OW) and Mtana (MTN), all of which are situated in the Eastern Cape Province. Three biomarkers, the acetylcholinesterase (AChE) assay, lipid peroxidation (LPx) assay, liver histopathology and a condition factor were used to determine sub-organism health and one bioindicator, the Estuarine Fish Community Index (EFCI), was used as a bioindicator of community health. The estuarine-dependent marine species Rhabdosargus holubi was selected as an indicator species for the sub-organism level analyses. The results from the community analyses indicated that the EK and OW estuaries were in 'good' condition, while the MTN was found to be in 'moderate' condition. Histological analyses revealed that R. holubi from all three estuaries showed signs of pathological changes to the liver, with the fish from the MTN eliciting the highest occurrence of these changes. The LPx assay found that R. holubi from both the OW and MTN showed signs of oxidative damage in the liver tissue, but those from the EK did not appear to be affected. The AChE assay showed that only the fish from the OW had been affected by anticholinesterase compounds. A laboratory study was undertaken using R. holubi as a positive control for the AChE and LPx assay. The fish were exposed to 3 μg/L chlorpyrifos, a known cholinesterase inhibitor, for six hours and their tissues were examined for changes to LPx levels and AChE activities. AChE activity was significantly inhibited (Mann Whitney U test, Z = 3.65, n = 38, P < 0.001) by the exposure, but LPx levels were not significantly affected. A composite index incorporating the biomarkers at different biological levels of organisation was developed. The index was designed to assist managers and scientists to determine whether the ichthyofauna of a system was being affected by environmental stressors and what management interventions could be undertaken to ameliorate the water quality in an estuary. The index was applied to the three estuaries investigated during the present study and both the OW and MTN were assessed to be in need of immediate management intervention. The fish in the OW were found to be stressed at all the sub-organism levels measured and the reason for this was hypothesised to be as a result of golf course activities in this adjacent estuary. A number of management actions are proposed to reduce the sub-organism stress observed in the fish from the OW. The livers of fish from the MTN were shown to be under stress; however the causative agent of this stress was unknown because there is no formal development in the MTN catchment. However, a possible contaminant source is proposed and management interventions to alleviate the stress on the biota of the MTN are suggested. The EK does not require immediate management intervention, however, continuous routine monitoring is recommended to ensure that conditions do not deteriorate. Shortcomings of the index were outlined and a number of suggestions were made in terms of other measures of biological health which could be incorporated into the index.