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Estuarine systems are of crucial importance to the provision of goods and services on a global scale. High human population densities in coastal systems have caused an increasing input of pollutants, of which nutrient pollution is of major concern. Increasingly, these areas are also impacted by physical disturbance, which can originate from anthropogenic sources (e.g. bait digging, shipping) or climate change causing increasingly frequent and intense storms. The individual impacts of such stressors on ecosystems have been investigated however their combined impacts have received less attention. Cumulative impacts of multiple stressors are unpredictable and will likely result in non-additive effects. Further, the effect of local environmental context on multiple stressors is a relatively understudied topic. Work in this thesis compared the combined impact of nutrient enrichment and physical disturbance in Scotland and Australia, using a series of manipulative field experiments. Results demonstrate that response to stressors is highly context dependent, varying between and within geographic locations. While the background levels of stress may vary, by comparing these two locations it is possible to comment on the adaptations and response that communities within different parts of the world display when subjected to additional stress. This study demonstrates that environmental context must be considered when implementing future management practices. Further work demonstrated that the impact of multiple stressors varies depending on how the stress is applied –whether stressors are applied simultaneously or whether there is a delay between two stressors. This study was among the first of its kind, assessing the implications of how multiple stressors react with each other given the order and intensity in which stressors were applied. Results demonstrated that systems can become sensitised to stress making them increasingly vulnerable to additional stress. Future research should be focussed on incorporating ecologically relevant scenarios of how stressors will impact estuaries while considering how environmental context will mediate impacts.

Microbiological water quality monitoring of bathing waters does not account for faecal bacteria in sediments. Intertidal deposits are a significant reservoir of faecal bacteria and this indicates there is a risk to human health through direct contact with the sediment, or through the resuspension of bacteria to the water column. This project investigated factors influencing the relative abundance of faecal indicator organisms (FIOs) in intertidal estuarine sediments. The effects of physical, biogeochemical and biological sediment characteristics, environmental variables and native microbial communities were explored through field campaigns on the Ythan and Eden estuaries, Scotland. The contributory role of sediments to adverse water quality was investigated by combining FIO abundance and measurements of sediment stability. The importance of strain and sediment characteristics in the adhesion of E. coli to suspended sediments was also examined using laboratory experiments. E. coli concentrations up to 5.9 log₁₀ CFU 100 g dry wt⁻¹ were observed, confirming that intertidal sediments are an important reservoir of faecal bacteria. The variability of E. coli abundance in estuarine sediments was successfully explained with multiple stepwise linear regression (Adjusted R² up to 87.4) using easily-obtainable measurements of sediment characteristics and environmental variables, with variability most heavily influenced by salinity and particle size gradients. Native microbial community population metrics and community constituent composition correlated with environmental gradients, but did not influence FIO abundance. The amount of E. coli adhering to suspended sediments ranged from 0.02 to 0.74 log₁₀ CFU ml⁻¹, and was dependant on strain characteristics and sediment type rather than zeta potential, with higher cell-particle adhesion at 2 and 3.5 PSU than 0 and 5 PSU. Monitoring of sediment characteristics will lead to more informed bathing water quality advisories to protect public health. Future research should focus on applying the findings here to the modelling of bacterial fate and transport on a catchment scale.

The Tay estuary is situated on the east coast of Scotland. The estuary is dominated by sediment biotopes, including mudflats which support sparse beds of two nationally scarce seagrass species, Zostera marina var. angustfolia (Hornem.) and Z. noltii (Hornem.). Seagrasses have been described as ecosystem engineers, shaping their sediment environment, and this may increase sediment deposition and stability. In this thesis the ecosystem engineering characteristics of seagrass habitats are explored. In 2008, the distribution of Zostera spp. in the Tay estuary was surveyed and mapped for the first time. Sediments within beds of Z. marina and Z. noltii were compared to investigate the influence of seagrasses on sediment characteristics. To explore the role of seagrass in sediment deposition and erosion, and coastal stability, sediment depth measurements were made in patches of Z. noltii, Z. marina and bare sediment over one year. The role of the root/rhizome system on sediment retention over winter was also considered. Sediment deposition in Z. noltii beds, and the influence of the plants on near-bed flow dynamics was further explored in the laboratory, using an 8 m seawater flume. In the field the retention of particles over 2 and 14 tides was measured, and the results of this experiment led to a study of the influence of leaf and sediment biofilms on particle retention, using the novel method of magnetic particle induction (MagPI). The efficacy of artificial seagrass beds and Z. noltii transplantation as habitat restoration techniques were compared over one year. During the trial, sediment deposition and changes in sediment characteristics were determined, and the protection given to saltmarsh cliffs fringing the study plots was assessed. Mechanisms underlying the results are suggested and the findings discussed. This study provides an insight into the ecology of seagrass in the Tay estuary and its role as an ecosystem manager. It may offer valuable data which could be utilised for future conservation policies, habitat restoration schemes and management planning of the area.