The primary source of nitrogen from agricultural activities in southern New England is application of fertilizers, on both land parcels (farms, the turf surfaces of lawns and golf courses) and cranberry bogs.

The bogs can be locally important; for example, they contribute three-quarters of the fertilizer nitrogen entering the Waquoit Bay watershed. Waste from livestock farming is an important source of nitrogen in some coastal regions, but in general is not sufficiently intensive to comprise a significant watershed input in southern New England. Fertilizer nitrogen applied today is often a product of the agro-chemical industry and is not simply recycled farm production, as it was most commonly on rural farms. Application rates of fertilizers vary depending on the land use. Some of the nitrogen in fertilizer volatilizes or otherwise escapes to the atmosphere; some is not taken up by the target plants and leaches to the groundwater. Heavy fertilizer use near the waterfront can add large amounts of fertilizer directly to a water body.