Faecal-indicator budget studies have shown marine bathing water quality at two small UK coastal resorts, Staithes and Newport, to be adversely affected by riverine inputs from lowland pastoral catchments (J. Chartered Inst. Water Environ. Mangt. 12 (1998) 414). The present paper reports on presumptive coliform (PC), presumptive Escherichia coli (PE) and presumptive streptococci (PS) concentrations at 43 sampling points on watercourses within these catchments, and on their relationship with land use and livestock-related management practices, such as grazing and slurry/manure applications. The results show >10-fold elevations in geometric mean faecal-indicator concentrations under high-flow conditions, compared with low flow, with maximum high-flow geometric mean PC, PE and PS concentrations of 2.6×10 6, 1.8×10 6 and 4.4×10 5 cfu/100 ml, respectively. High-flow geometric mean concentrations exhibit highly significant positive correlations with land use/management variables associated with intensive livestock farming, both within the individual catchments and in the two combined. Additional factors, such as antecedent weather conditions and topography, contribute to inter-catchment variability in water quality. Although inputs from diffuse and point sources of pollution were not quantified, point sources (e.g. runoff from farm yards) seem likely to be significant. The findings suggest that it may be possible to develop generic statistical models to predict microbial water quality from land use and farm management data. They also provide indirect evidence that channel bed sediment ‘stores’ closely reflect land use within their catchments and that there is little die-off of organisms along watercourses.