It is widely recognized that anthropogenic activities have resulted in significant changes to the ecology and hydromorphology of riverine ecosystems globally. Across much of lowland England a number of riverine habitats and the flora and fauna inhabiting them, have been lost or disadvantaged by historic channel modifications. Many of the most significant modifications took place in the decades following World War II, in a drive to increase food security through improved land drainage and associated flood management. A better understanding of the geomorphological, hydrological and biodiversity elements that have been compromised or lost is required in order to characterise the benefits of planned measures to restore and reinstate channel form and function for EU WFD, Habitats Directive and other conservation designations (e.g. SSSI condition assessments). To generate this understanding in an environment where natural processes have been impacted over large spatial scales, an innovative palaeoecological approach is employed in this thesis that provides a window on historic riverine ecology and habitat conditions so that the contemporary channel and community inhabiting it can be gauged prior to the implementation of river restoration programmes. The analysis of historic archival material (maps, photographs, local authority and management records), and the detailed investigation of sedimentary records and sub-fossil insect remains (Trichoptera, Coleoptera and Gastropoda) associated with in-channel bars, weirs, bridges and palaeochannels is used in this thesis in order to achieve this. These records will provide data regarding changes to the aquatic macroinvertebrate community and instream hydromorphology within specific reaches/biotopes/habitats subjected to historical physical modification. The historic data (documents and palaeoenvironmental data) is analysed in parallel with contemporary data on instream habitats and faunal community composition to define benchmark conditions on three Site of Special Scientific Interest rivers. This approach enables a comparison between past and present channel hydromorphology and the instream faunal communities. The characterisation of benchmarks provides a baseline for future conservation and restoration policies within riverine ecosystems that can be used to help define pre-impacted or reference conditions. The research presented in this thesis has relevance to the conservation objectives of rivers with special designations (e.g. SSSI and Habitats Directive) for wildlife and to meeting the wider requirements of the Water Framework Directive.

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Most rivers and streams in England and Wales have been channelised for reasons of flood control, drainage of wetlands and channel improvement for navigation. Channelisation is one of the most dramatic aspects of man's impact on the riverine system. It involves the direct modification of the river channel and has impacts on the environment and ecosystem of the river. In order to decrease or ameliorate the impacts of channelisation and restore the riverine habitat, different restoration and rehabilitation techniques are used. Improvement structures in a river may produce many effects, but their overall function is to increase the diversity of the river habitat. Although the initial objectives of the installation of such structures are improvements to fish stocks and fisheries, they also improve biodiversity in invertebrates and plants and hence increase the conservation value. The effectiveness of two river habitat improvement techniques; artificial riffles and current deflectors, installed in two rivers. Harper's Brook and the River Smite were studied by comparing the macroinvertebrate communities of a control site on each river with those of channelised and improved sites by means of benthic kick-sampling. Eighty four samples from seven sites of Harper's Brook and 57 samples from five sites of the River Smite were collected in four seasons. One hundred and eight taxa with the total abundance of 210,045 from Harper's Brook and 101 taxa with the total abundance of 149,397 from the River Smite were identified. The results of ANOVA showed that the sites in Harper's Brook were significantly different in mean diversity (H') and in general the mean diversity of natural and two artificial riffles were greater whilst those of run sites were smaller. The natural riffle of the River Smite had also the greater mean diversity than the other sites. The results of DECORANA indicated that there was a clear separation between the riffle sites and run sites in all seasons in Harper's brook, and the separation of the natural riffle from the other sites in the River Smite. The results of TWINSPAN agreed with DECORANA, indicating that the two artificial riffles were associated with the natural riffle and the third with the run sites. The overall results showed that the riffle reinstatement was successful in improving the hydrology and biology of some sites close to or similar to that of a natural site. Current deflectors have also been successful in changing the hydrology of the river and creating pool and shoal sequences. Although the biology of the created shoal was not comparable to the natural riffle, it had a better biology compared with an unimproved site.

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In this thesis I investigate the complex relationships between society, economy and nature taking place in the Amazon estuary, Northern Brazil. Throughout this work I use remote sensing data and techniques combined within the ecosystem services framework. Chapter 2 identifies the broad research gap concerning the effective assimilation of remote sensing into ecosystem services research. It provides a summary of what has been done, what can be done and what can be improved upon in the future to integrate remote sensing into ecosystem services research, laying out the main problems that are developed in the following chapters using the Amazon estuary as a case study. In chapter 3 I analyse the recent and increasing observed trends in forest cover change and ecosystem services as consequence of the interactions between political, economic and social factors. Through a cross-methodological approach, this section of the thesis exposes the political frontiers of forest cover change in the estuary and explores the spatially-explicit relationships linking the Green Vegetation Cover (GVC) to the availability of ecosystem services provided by forests. Such complex relationships are then captured by using an innovative approach used in economics to capturing the relationships between time-delayed variables. Chapter 4 presents the analysis of several time series in order to compare the case of the Amazon estuary to other similar relevant cases elsewhere in the world, providing important insight into the dynamics of social-ecological systems. This chapter, summarises and explore the state of slow and fast variables, observed drivers of change and recent trends in the Amazon, Mekong and Ganges Brahmaputra-Meghna deltas. The results show that there are various fundamental changes in many key ecosystem services, pointing to a changing dynamic state and increased probability of systemic threshold transformations in the near future. In chapter 5 I integrate a large and comprehensive set of social and economic context variables, aimed at understanding land use/cover transition processes in the Amazon estuary over the last three decades and how these might influence the estuarys landscape in the future. In this chapter I develop and apply an integrated modelling approach to capture intricate dynamics in the estuary. The results show that the modelling approach was able to identify and capture specific regional land/use cover dynamics in estuary, simulating the dynamic competition amongst different land use types under different scenarios.

The collection of scales is common when fish communities are sampled within research and monitoring programmes in freshwater fisheries. Although used primarily to age individual fish, there is increasing evidence of their potential for application to other ecological methods, yet there is also considerable uncertainty in how this can be achieved. Thus, the purpose of this research was to examine how the use of scales within age and growth studies can be enhanced and investigate their application to freshwater trophic ecology, with a particular focus on advancing their utilisation within stable isotope analysis (SIA). The research used fishes of the Cyprinidae family as the focal species. Cyprinids are of substantial global, socio-economic importance as their communities are valued ecologically, commercially and recreationally. The research assessed current methodologies, highlighted extant gaps in knowledge and sought to resolve these issues. It covered work regarding the intrinsic error contained in estimating fish age from scales and improved scale application within SIA through the provision of key data that is currently lacking within the literature. An initial invasion ecology case-study provided new insights into the growth and trophic impacts of a model native and two non-native fishes under three distinct approaches of differing spatial scale and complexity. The results revealed a range of ecological consequences for the native species from the invaders, although the extent of these was also a function of spatial scale. Additionally, a number of procedural concerns relating to the collection of fish age data and current SIA methodologies were highlighted. The use of scales to derive estimates of the ages of fish is well established, with outputs used to address questions on aspects of fish and fisheries ecology, but the process remains prone to inherent errors. The research revealed that precision of growth estimates is significantly influenced by the sub-sampling regime applied. Where individuals are long-lived and slow-growing, sub-sampling strategies that result in few scales being analysed produced imprecise data and potentially erroneous outcomes. Additionally, uncertainty in the accuracy of ageing scales also potentially results from subjective interpretation of scale features. A statistical model was developed to incorporate this uncertainty into analyses, using Bayesian statistics and a bootstrapping methodology, to improve age and growth rate estimates. The model successfully produced error adjusted von Bertalanffy growth parameters. Food web and trophic analyses have traditionally been completed through stomach content analysis, but increasingly SIA is preferred, as it provides greater temporal perspectives and requires smaller sample sizes. In fish studies, dorsal muscle tissue is typically favoured, but this is often collected destructively. The research revealed that non-destructively collected tissues, such as scales, can act as a proxy for muscle and their isotopic values can be converted with minimal error when species-specific factors are used. When stable isotope data are applied to dietary studies, their use in statistical mixing models requires accurate step-wise enrichment values between diet and consumer (i.e. discrimination factors). There is considerable uncertainty in the variability of discrimination factors between species and the influence of their diet. Consequently, specific diet-tissue discrimination factors were produced for a range of cyprinid species and diet was shown to significantly affect diet-tissue discrimination. The application of species-specific values within mixing models can result in significant differences when compared with using standard values and consideration of the influence of diet needs to be made when investigating omnivorous species. The rate of turnover of carbon and nitrogen stable isotopes was also determined and variability between tissues was revealed, indicating that species- and tissue-specific half-lives should be considered when deciding upon experimental time-frames. In summary, the research has provided substantial information targeting extant knowledge gaps relating to the application of scales from cyprinid fishes to ecological studies. Regarding fish age and growth, issues surrounding accuracy and precision of estimates has been tackled, informing researchers of the influence on precision of applying sub-sampling regimes to subsequent growth analyses and providing an original statistical tool that can improve accuracy through producing growth parameters that better reflect inherent errors in fish age data. In contributing to the use of scales in SIA, novel data have been provided that will reduce the requirement for destructive sampling of fishes and enhance present understandings of the significance of species- and tissue-specific discrimination factors and turnover rates.

The ecology and proximate composition of some plants and animals in running waters were studied in an attempt to elucidate some aspects of the relationships between different trophic levels. Although algal communities almost always showed a spring bloom, apparently in response to increasing day length, the standing crop subsequently showed considerable variation. This was often attributable to such factors as either the direct or indirect effects of flooding or to the interactions between communities. No marked seasonal trends were observed in the amount of lipid found in algae from field collections, contrasting with the situation in the larval lamprey, a microherbivore. Algae generally made only a small contribution to the total organic fraction of the suspended and epilithic material. Although the microflora formed an important component of the diet of Asellus and Gammarus, only in the case of Paramecium were microphagus feeders apparently effecting the standing crop. Lampreys accumulated large neutral lipid reserves at the end of both the larval microphagous and adult carnivorous stages, an adaptation to the metabolic demands of the subsequent lengthy non-trophic phases. The vertical distribution, degree of motility and seasonal changes in the biology of various crustacean species were important in determining their use as a teleost food source. Other factors affecting fish feeding were hunting behaviour, visual acuity, mouth morphology and dimensions, and the temperature and turbidity of the water.

Ecological degradation of rivers and streams resulting from multiple stressors is a big concern in the UK and other countries all over the world. The two largest stressors introduced by agriculture are phosphorus and fine sediment. The combined impacts of the multiple stressor and relative strength of each individual stressor needs to be understand. A Number of ecological response variables were tested through a field mesocosm experiment, including algal and ecosystem variables: (1) The subsidy-stress for phosphorus and sediment (where at first, an ecological variable increases positively with the increased level of phosphorus and sediment until very high levels are reached, when negative effects would be expected); (2) Whether the stressors work individually or as multiple stressors and whether they interact; (2.a) Three ecological guilds of algae (‘low profile’ growth form, ‘high profile’ growth form, ‘motile’ growth form) were used in order to test whether the high profile growth form decreases and motile growth form increases with increase of sediment deposition, or whether (2.b) Both high profile growth form and motile growth form increase with increase concentration of phosphorus. Most species showed subsidy stress responses for the gradient of phosphorus, but for the gradient of sediment the response was negative. Phosphorus and sediment together generally acted as multiple stressors and usually in a simple additive way, but complex interactions were also found. The algal community was impacted synergetically by phosphorus and sediment, as shown by the field study. The combined results from the field study and the mesocosm experiment indicate that phosphorus and sediment should be managed together in view of their acting most of the time as multiple stressors in their impacts on epilithic algae. Finally, in order to have a better evaluation for the possible reasons of a stream health decline, it is strongly recommended to measure routinely both fine sediment and phosphorus in the future.

The alternation of bathymetrlc lows (pools) and highs (riffles) along a stream plays a critical role in ecology. Besides providing a diversity of substrate material and local flow velocities, pool-riffle sequences (PRS) influence the living conditions in the near-stream sediments by inducing an infiltration of surface water Into the subsurface and a delayed exfiltration back to the stream. This process, called hyporheic exchange flow (HEF). supplies oxygenated water to subsurface organisms and has the potential to modify the chemical composition of stream water. Although PRS-induced HEF is to some degree predictable, little is known about its potential variability in time, space, and across scales. The research reported here investigates this gap through field experimentation in low flow conditions, and numerical modelling. First flow characteristics are detailed through extensive in situ measurements conducted at the metre-scale, and across a range of temporal resolutions. The geometry of the subsurface flow systems, residence time distributions, and fluxes are then estimated through three-dimensional groundwater modelling. Using these models, a sensitivity analysis is performed to characterize the influence of identified controls on HEF characteristics. Finally through a hypothetical 2·D model of a pool-riffle sequence, we evaluate the consequences of Ignoring small scale exchange flow induced by current-obstacle interactions, in channel-unit scale models. This study was conducted at the River Leith, a third-order stream situated within the Eden catchment, in the north west of England. The field site is located in the lower part of the catchment, and belongs to a three kilometre stretch that is known to be significant1y groundwater-fed by the underlying Permo-Trlassic sandstone. In summer, the stream's discharge can be as low as 0.03 m3 S -l. The 200 m study reach includes a succession of three pool-riffle sequences, located along a meander. The streambed consists primarily of gravels and cobbles. The first study examines at a high spatial and temporal resolution the variability of hydraulic conductivity (K), vertical hydraulic gradients (VHGs), and subsurface fiuxes, over a single riffle- step-pool sequence. A 20 m reach was equipped with a network of piezometers in order to determine the distribution ofVHGs and K. During a summer month, temporal variations ofVHGs were regularly surveyed and, for a subset of piezometers, the water level was automatically recorded at 15 min intervals by logging pressure transducers. Additionally, point-dilution tests were carried out on the same subset ofpiezometers. Whereas the distribution of vertical fluxes can be derived from K and VHG values, point-dilution tests allow for the estimation of horizontal fluxes where no VHG is detectable. Results indicate that, spatially, VHGs switched from upwelling to downwelling across lateral as well as longitudinal sections of the channel. Vertical fluxes appeared spatially more homogeneous than VHGs, suggesting that the latter can be a poor indicator of the intensity of flow. Finally, during flow events (high flows), some VHGs showed little or no fluctuations. This was interpreted as the result of a pressure wave propagating from upstream through highly diffusive alluvial sediments.