Watershed nutrient management often focuses on actions that reduce the movement of nitrogen (N) and phosphorus (P) from agricultural lands into streams. One area of management focus is the buffer of land adjacent to streams. Wetlands and forests in this buffer can intercept and retain N and P from the landscape. In addition to directly intercepting agricultural nutrients, natural habitats in the buffer can alter stream geomorphology and influence the in-stream processing and transformation of N and P to less labile and mobile forms. Here, we assess the influence of buffer land cover on in-stream processing of N and P. We measured nutrient dynamics in the water column and sediments of agricultural streams in the Fox River and Duck Creek watersheds (WI, USA) during the growing season. In these streams, water column processing was low, possibly due to a lack of primary producers in the water column. Water column P processing was weakly associated with wetland land cover in the buffer, but buffer land cover had no clear effect on inorganic N processing. On the other hand, sediments were almost always a source of inorganic P and a sink for inorganic N. Sediment P release was higher in streams with more agricultural land cover in the buffer. Sediments in streams with agricultural land cover in the buffer also removed more nitrate, even after accounting for the greater availability of nitrate in those streams. The buffer land cover conditions we quantified occupy a very small portion of the overall watershed (100 m wide, for 1 km upstream of the study site) but nevertheless appear to influence in-stream cycling of N and P. For P management, reducing agricultural land cover in buffers is already a priority due to the ability of wetlands and forests to intercept nutrients, but this study suggests there may be some additional benefit due to changes in in-stream P processing.