Estuarine environments are biologically productive ecosystems that are both economically and socially important. Consequently, a decline in the microbiological water quality can pose a risk to human health and have severe socioeconomic consequences, especially for areas that rely on tourism and shellfisheries for income. The enumeration of faecal indicator bacteria (FIB) in water samples has been the paradigm for estimating water quality in coastal zones, but there is an emerging view that sediments are a poorly studied and yet a significant reservoir of FIB. The aims of this thesis were: (I) to investigate the role of sediments as a reservoir for FIB and other potentially pathogenic bacteria; (II) to examine the spatial ecology of FIB in relation to sediment composition (grain size and organic matter content); (III) to investigate the influence of point and diffuse pollution sources on the abundance of bacteria in marine and estuarine sediments; (IV) to investigate the abundance of human pathogenic bacteria in the Conwy estuary, North Wales, UK, and (V) to investigate the influence of suspended particulate matter (SPM) on the survival of FIB in both fresh and brackish water. Culturable E. coli, total coliforms, enterococci (FIB), Salmonella, Campylobacter, Vibrio spp. and heterotrophic bacteria were enumerated in sediments and water from the Conwy estuary that is subject to various point and diffuse sources of pollution. FIB counts were three orders of magnitude greater in sediments compared with the overlying water column, demonstrating that estuarine sediments are a significant reservoir for FIB and other potential pathogens. In addition, sediment grain size analysis and organic matter content determinations revealed that finer sediments such as clay, silt and very fine sand contained significantly higher concentrations of all bacterial groups enumerated. The enumeration of FIB in marine sediments surrounding an offshore sewage outfall pipe revealed that spatial variations in FIB abundance reflected the course of the sewage effluent plume as predicted by a hydrodynamic model, demonstrating the impact of point sources of microbial pollution on the underlying sediments. To address the actual pathogen content of sediments in the Conwy estuary (rather than only indicator bacteria), PCR and qPCR were utilized to detect and quantify known pathogen virulence genes, revealing that estuarine sediments are a reservoir for pathogenic bacteria. Furthermore, qPCR suggested greater concentrations of FIB compared with culture counts from the same sample, indicating the possible presence of viable but non-culturable (VBNC) bacteria. Consequently, sediment-associated bacteria pose a risk to human health if they are resuspended into the water column under certain hydrodynamic processes, as tide-dominated estuaries usually contain large areas of fine sand that are easily mobilized. To investigate the influence of SPM concentration on FIB survival, fresh and brackish water containing low (~16 mg/l), high (~160 mg/l) and extreme (~1650 mg/l) SPM concentrations were inoculated with crude sewage and sheep faeces. FIB were enumerated every 24 hrs for 5 days, revealing that SPM concentrations influence FIB survival in brackish water but had minimal influence in freshwater over time. In general, FIB concentrations increased with a decrease in SPM concentration. These data add to a limited body of evidence on the role of sediments as a reservoir for pathogenic bacteria, with implications for routine monitoring protocols that assess the microbial pollution of environmental waters. In addition, these data suggest that catchment-based risk assessments of microbial pollution in aquatic systems should consider the source of FIB, the hydrodynamics of the environment, and the subsequent influence of SPM concentrations, all of which determine the survival of FIB in aquatic environments.