Abstract: Acidification was categorized as the main environmental problem in Scandinavia during the 1960’s. Fortunately for Sweden, as with other countries in Scandinavia, has shown a process of recovery from acidification, by emission control. Further Sweden has had an extended liming program to mitigate the effects from acidification. Regarding the acidification assessment of the EU Water Framework Directive, it requires that EU members attain a ‘good ecological status’ in their surface waters. The status is defined as a deviation from a reference value and this is achieved using a reference reflecting a preindustrial state. As the waters are recovering from acidification the liming program can be reduced. Hence, there is a need to develop tools that can be used for decisions to stop liming in single waters. This study states three approaches: the well known hydrochemical model MAGIC, a meta-MAGIC model which calibrates the reference value computed by MAGIC model and paleolimnology studies. The latter is the key because it is the one that measures the reference value by immediate samples insitu. However, all methods have advantages and disadvantages, which allowed the development of an additional tool called meta-paleo for the same purpose. This meta-paleo model is designed based on an 11 years mean of contemporary water chemistry and paleolimnology data of 71 lakes. This tool for acidification assessment enables to work with few parameters of water chemistry. However it is concluded that the model has uncertainties, which should be evaluated so it can be used as a tool for decision making.

Les milieux côtiers subissent de fortes pressions dues aux activités anthropiques. Ces pressions vont parfois impacter les écosystèmes benthiques. En Europe, des réglementations internationales, telle que la Directive Cadre sur l’Eau (DCE), ont vu le jour. La DCE a fixé un cadre pour obtenir le retour et le maintien d’un bon état écologique pour les masses d’eau côtières, jusqu’à un mile de la côte. Pour vérifier si ce bon état écologique est atteint, des outils de mesure adaptés et performants sont nécessaires. L’utilisation d’indices biotiques basés sur les faunes de foraminifères benthiques est un des moyens pour mesurer l’état des écosystèmes. Ces indices basés sur les faunes de foraminifères sont en pleine expansion, notamment en Méditerranée. En termes de méthodologie, nous avons pu améliorer une technique de concentration des foraminifères benthiques par séparation par densité, qui accélère le traitement des échantillons. L’indice TSI-Med a la particularité d’apporter une correction pour l’état trophique naturel, c’est-à-dire le taux d’enrichissement naturel en matière organique, sur la base de la granulométrie du sédiment. Nos données suggèrent néanmoins que cette correction est encore insuffisante. Nous avons également comparé plusieurs indices biotiques basés sur les faunes de foraminifères benthiques le long des côtes méditerranéennes françaises. Les indices basés sur la diversité, notamment l’exp(H’bc), ne sont pas adaptés à notre zone d’étude oligotrophe. Les indices basés sur les groupes écologiques d’espèces que nous avons testés (TSI-Med, Foram-AMBI et FSI) sont plutôt bien corrélés. Le principal facteur qui va induire des différences entre ces indices est la liste d’assignation écologique des espèces. Trop d’espèces n’ont pas encore été assignées et l’assignation de plusieurs espèces majeures est problématique. Néanmoins, nous avons montré que ces indices sont efficaces à détecter l’impact d’un enrichissement en matière organique diffus et/ou provenant de source ponctuelle, telle que les rejets de stations d’épuration (côte israélienne). Pour perfectionner ces indices, des efforts de caractérisation écologique des espèces doivent être poursuivis. / Coastal environments suffer from anthropogenic activities. Various types of pressure can have large impacts on benthic ecosystems. In Europe, international regulations, such as the Water Framework Directive (WFD), have been implemented. The WFD aims to attain and sustain a good ecological status for all coastal waters, up to one mile from the coast. To verify whether this good status has been reached, adapted and efficient measuring tools are needed. The use of biotic indices based on foraminiferal faunas are a mean to assess the ecosystem status. The use of indices based on foraminiferal faunas rapidly increases, especially in the Mediterranean. In terms of methodology, we were able to improve a method to concentrate benthic foraminifera by density separation, which accelerates the sample treatment. The TSI-Med index includes a correction to take into account the natural trophic state, i.e., the natural enrichment rate in organic matter, on the basis of sediment grain size. However, our data suggest that the applied correction is still insufficient. We also compared several biotic indices based on benthic foraminiferal faunas along the French Mediterranean coast. Indices based on diversity, such as the exp(H’bc), are not suited for our oligotrophic study area. The results of three tested indices based on ecological groups (TSI-Med, Foram-AMBI, FSI) are well correlated. The main factor inducing differences between the indices is the list of ecological assignments for the various species. In general, too many species have not yet been assigned to ecological categories and the assignment of several major species is problematic. Nevertheless, we show that the indices are already efficient in detecting the impact of diffusive organic matter enrichment or enrichment from point sources, such as sewage outlets (Israelian coast). To further perfection the foraminiferal indices, the efforts of ecological assignments of species have to be continued

The European Water Framework Directive 2000 established a new emphasis for the management of freshwaters by setting ecologically-based water quality targets that are to be achieved through holistic, catchment-scale, ecosystem management. However, significant knowledge gaps exist in the understanding of the cumulative effectiveness of multiple mitigation measures on a number of pollutants at a catchment scale. This research contributes to improved understanding of the effectiveness of an ecosystem management approach to deliver catchment-scale water quality improvements on the National Trust Holnicote Estate on Exmoor, UK. This research is part of a larger multi-objective project funded by the UK Department for Environment, Food and Rural Affairs (Defra), to demonstrate the benefits of land use interventions for the management of flood risk. This thesis evaluates the effects of upland ditch blocking on physico-chemical and biological parameters of water quality in an upland Horner Water catchment one year after habitat restoration, and establishes a solid baseline for the monitoring of the effects of current and future land management changes in a lowland, intensively managed, agricultural Aller catchment. The spatial variability of soil physical and chemical properties (bulk density, total carbon (TN), nitrogen (TN), C:N ratio, δ15N, total phosphorus (TP), inorganic phosphorus (IP), organic phosphorus (OP)) and water quality determinands (suspended sediment (SS), dissolved organic carbon (DOC), total particulate carbon (TPC), total oxidised nitrogen (TON) and dissolved reactive phosphorus (DRP)) in the two study catchments with contrasting land use has been characterised and linked to the prevailing land use. Agricultural land use resulted in extensive homogenisation of soil properties. The spatial dependence of all soil properties, except for bulk density and δ15N, was stronger in the agricultural than the semi-natural catchment (nugget:sill ratio 0.10-0.42 in the Aller and 0.15-0.94 in Horner Water), while bulk density, TP, inorganic phosphorus (IP), organic phosphorus (OP), C:N ratio, δ15N and carbon storage showed a longer range of spatial auto-correlation in the agricultural catchment (2,807-3,191 m in the Aller and 545-2,599 m Horner Water). The central tendency (mean, median) of all soil properties, except for IP and δ15N, also differed significantly between the two catchments (P < 0.01). The observed extensive alteration of soil physical and chemical properties in the agricultural catchment is likely to have long-term implications for the restoration of ecosystem functioning and water quality management. The intensive land use seems to have resulted in an altered ‘catchment metabolism’, manifested in a proportionally greater total fluvial carbon (dissolved and particulate) export from the agricultural than the semi-natural catchment. The agricultural catchment supported significantly higher DOC concentrations (P < 0.05) and the quality of DOC differed markedly between the two study catchments. The prevalence of more humic, higher molecular weight compounds in the agricultural catchment and simpler, lower molecular weight compounds in the semi-natural catchment, indicated enhanced microbial turnover of fluvial DOC in the agricultural catchment as well as additional allochtonous terrestrial sources. During an eight month period for which a comparable continuous turbidity record was available, the estimated SS yields from the agricultural catchment (25.5-116.2 t km2) were higher than from the semi-natural catchment (21.7-57.8 t km2). Further, the agricultural catchment exported proportionally more TPC (0.51-2.59 kg mm-1) than the semi-natural catchment (0.36-0.97 kg mm-1) and a similar amount of DOC (0.26-0.52 kg mm-1 in the Aller and 0.24-0.32 kg mm-1 in Horner Water), when normalised by catchment area and total discharge, despite the lower total soil carbon pool, thus indicating an enhanced fluvial loss of sediment and carbon from the intensively managed catchment. Whilst detection of catchment-scale effects of mitigation measures typically requires high resolution, resource-intensive, long term data sets, this research has found that simple approaches can be effective in bridging the gap between fine scale ecosystem functioning and catchment-scale processes. Here, the new macro-invertebrate index PSI (Proportion of Sediment-sensitive Invertebrates) has been shown to be more closely related to a physical measure of sedimentation (% fine bed sediment cover) (P = 0.002) than existing non-pressure specific macro-invertebrate metrics such as the Lotic Index for Flow Evaluation (LIFE) and % Ephemeroptera, Plecoptera & Trichoptera abundance (% EPT) (P = 0.014). Further testing of PSI along a pronounced environmental gradient is recommended as PSI and % fine bed sediment cover have the potential to become a sensitive tool for the setting and monitoring of twin sedimentation targets. Upland ditch management has not had any discernible effect on water quality in the semi-natural upland catchment one year after restoration, which may be due to the short-term post-restoration monitoring period but may also reflect benign effects of large-scale earth moving works on this high quality environment. The conceptual understanding of catchment processes developed in this thesis suggests that cumulatively, the recently completed mitigation works in the lowland agricultural catchment will likely result in reduced sediment and nutrient input into the aquatic environment. However, further research is needed to build on this detailed baseline characterisation and inform the understanding of the effectiveness of combined mitigation measures to reduce the flux of multiple contaminants at the catchment scale.