Faecal bacteria exist in both free-living and attached forms in estuarine waters. The deposition of sediments can take faecal bacteria out of the water column and to the bed. The sediments can subsequently be re-suspended to the water column, which can then lead to re-suspension of the faecal bacteria of the attached forms back to the water column. Therefore, the fate and transport of faecal bacteria is highly related to the governing sediment transport processes, particularly where these processes are significant, such as the Severn Estuary, UK. However, little attempt has been made to model such processes in terms of predicting the impact of the sediment fluxes on faecal bacteria levels. Details are given of the refinement of a numerical model of faecal bacteria transport, where the sediment transport processes are significant. After testing the sediment-bacteria interaction model favourably against known results in previous study, the model was applied to the Severn Estuary and Bristol Channel, UK, to investigate the impact of suspended sediment fluxes on the corresponding faecal bacteria transport processes. The model predictions have proved to be encouraging, with the results being compared to a traditional faecal bacteria modelling approach, where sediment bacteria interactions were not included. The new model provides improved predictions of faecal bacteria concentrations when sediment transport is included and for the Bristol Channel Severn Estuary it can be seen that the effects of the sediments on the bacterial levels in the water column can be significant.