The water quality deteriorations in river and estuarine waters are a global issue. Particularly, the water quality impairment due to contamination of Faecal Bacteria Indicator, such as E. coli and Faecal Coliform in river channel, estuary bathing and shellfish waters are of special interests due to potential risks to human health. These indicators are important in water quality assessment outlined in both EU Water Framework Directive and US Clear Water Act. The hypothesis of the study is that the global climate change and intensive farming would cause severe deterioration to faecal coliform levels in these water bodies. Approaches to quantify these impacts are carried out with numerically modelling through catchment model Soil and Water Assessment Tool (SWAT) and hydrodynamic model DIVAST with the focus in the coastal catchment of river Frome and Piddle connected to a natural harbour in Dorset, southern England.