The objective was to investigate the potential risk of faecal indicator organism (FIO) bacteriological contamination of river catchments and coastal bathing waters from farm management practices and to develop practices to reduce the risk. A risk assessment on 117 farms was carried out in two river catchments in south-west Scotland. Manure storage facilities, farming practices, field conditions and catchment characteristics were assessed. River samples at 33 locations were regularly taken and analysed for FIOs. Available manure storage capacity and farm management practices are inadequate on a high proportion of farms and FIO contamination of watercourses was likely the result of effluent transported into watercourses due to non-collection or poor containment. In addition, surface run-off or leaching following land application of manure or intensive stocking in adverse conditions was a high risk on up to 50% of farms. The concentrations of FIOs in the streams of two sub-catchments with high livestock intensity was 4 to 8 times higher compared to the two sub-catchments which had a low livestock intensity. The majority of potential risks of agricultural pollution to watercourses may be eliminated through improved manure and dirty water management, forward planning of manure spreading activities and improved operational procedures.