The proper recognition and calculation of polluted sources and the fate and transport of faecal organisms in catchments, river networks and coastal waters are very important to the assessment of environmental exposure, health impacts and risk perceptions of faecal indicator organisms (FIO) in coastal waters. The paper reviews the integrated modelling techniques for faecal processes from cloud to coast, including sediment and faecal bacteria interactions, and then presents a theoretical and case study in the numerical modelling for FIO levels in the river Ribble and Fylde Coast using the twodimensional or three-dimensional environmental fluid dynamics code and the 1D Flow And Solute Transport in Estuaries and Rivers models, respectively. The related key parameters in the linked model are illustrated and analysed, together with validation of the hydrodynamic processes and the faecal bacteria concentration levels being undertaken using measured related data acquired in 1999. Using the model results, a quantitative microbial risk assessment is undertaken, where a moderate dose for swimming in faecal coliform-laden flows is accepted, as given by the European (EU) water quality standard requirements. The results show that some local regions of relatively high concentration exist near the outfalls and these values are not compliant with the mandatory and tighter microbial standards in the UK, as governed by the new EU Water Framework Directive. Finally, some new research and key challenges for the future are discussed in the paper.