In spite of increasing efforts to reduce nitrogen inputs into groundwater from intensive agriculture, nitrate (NO3) remains one of the major pollutants of drinking-water resources worldwide. Determining the source(s) of NO3 contamination in groundwater is an important first step for improving groundwater quality by emission control, and it is with this aim that we investigated the viability of an isotopic multi-tracer approach (δ15N, δ11B, 87Sr/86Sr), in addition to conventional hydrogeologic analysis, in two small catchments of the Arguenon watershed (Brittany, France). The main anthropogenic sources (fertilizer, sewage effluent, and hog, cattle and poultry manure) were first characterized by their specific B, N and Sr isotope signatures, and compared to those observed in the ground- and surface waters. Chemical and isotopic evidence shows that both denitrification and mixing within the watershed have the effect of buffering NO3 contamination in the groundwater. Coupled δ11B, δ15N and 87Sr/86Sr results indicate that a large part of the NO3 contamination in the Arguenon watershed originates from the spreading of animal manure, with hog manure being a major contributor. Point sources, such as sewage effluents, contribute to the NO3 budget of the two watersheds.