Shellfish have been recognised as an important human food source since roman times and are now routinely consumed by inhabitants across five continents. However, shellfish are also well known vectors for human illness as they are capable of bio-accumulating pathogenic micro-organisms from the wider environment within somatic tissues and hence, are capable of transferring these pathogens into the human food chain. Current European efforts to safeguard consumers include the routine bacteriological monitoring of shellfish tissues using E. coli as a proxy for potential pathogenic micro-organisms. The aims of this thesis were firstly, to identify and quantify the bacterial reservoirs present in commercial shellfish harvesting areas. Secondly, to determine the relative contribution of these reservoirs under different mitigation techniques, and thirdly, to examine the relationship between the bacterial and viral reservoirs present within shellfish tissues. A single commercial mussel (Mytilus edulis) bed was intensively surveyed to identify both spatial and temporal changes in the bacterial reservoir present within mussel tissues and to examine the relationship between the bacterial reservoir present within the mussel tissues and concentrations of bacteria present in the underlying sediment. This study concluded that the underlying sediments represented a greater bacterial reservoir than within the mussel tissues, however no spatial relationship between the two reservoirs was evident. In addition, we investigated the potential of epizoic organisms to act as a bacterial reservoir. The findings from this study demonstrated that epizoic barnacles contained more than 80% of the total coliform bacteria present and, as such, represent a previously unidentified, but significant bacterial reservoir in shellfish harvesting areas. Based on previous findings, the effect of standard mitigation techniques i.e. depuration and offshore relaying on the previously identified bacterial reservoirs were investigated. A standard 48 hour depuration treatment was shown to be effective in the reduction of indicator bacteria from shellfish tissues, but ineffective in reducing the bacterial content of epizoic organisms to beneath acceptable levels. Offshore relaying was shown to be an effective measure to reduce both bacterial and viral concentrations in shellfish tissues, however, these concentrations demonstrated no relationship with the bacterial content of the surrounding waters. Finally the relationship between the bacterial and viral content of shellfish tissues was examined and compared to modelled E. coli concentrations in the water surrounding a sewage outfall. No relationship between the bacterial and viral content of the shellfish was observed. This finding supports previous studies suggesting that bacterial indicators are poor surrogates for viral contamination of shellfish. However, interestingly the determined concentrations of norovirus within shellfish tissues were more closely correlated with the modelled predictions than the determined E. coli concentrations from the shellfish tissues. In conclusion, the bacterial reservoir within shellfish flesh may be over-shadowed by larger bacterial reservoirs present within the wider shellfish harvesting area. The interaction between these environmental bacterial reservoirs and the bacterial reservoirs within shellfish flesh remains largely unknown, and represents an area for further study, especially with regard to the impact of alternative environmental bacterial reservoirs on the bacterial content of shellfish destined for human consumption.