Reservoirs often receive excess nitrogen (N) and phosphorus (P) lost from agricultural land, and may subsequently influence N and P delivery to inland and coastal waters through internal processes such as nutrient burial, denitrification, and nutrient turnover. Currently there is a need to better understand how reservoirs affect nutrient transport in agricultural landscapes, where few prior studies have provided joint views on the variation in net retention/loss among reservoirs, the role of reservoirs apart from natural lakes, and differences in effects on N versus P, especially over time frames >1 year. To address these needs, we compiled water quality data from many rivers in intermediate-to-large drainages of the Midwestern US, including tributaries to the Upper Mississippi River, Great Lakes, and Ohio River Basins, where cropland often covers >50 % of the contributing area. Incorporating 18 years of data (1990–2007), effects of reservoirs on river nutrient transport were examined using comparisons between reservoir out- flow sites and unimpeded river sites (N = 869, including 100 reservoir outflow sites) supported by mass balance analysis of individual reservoirs (n = 17). Reservoir outflows sites commonly had 20 % lower annual yields (mass per catchment area per year) of total N and total P (TP) than unimpeded rivers after accounting for cropland coverage. Reservoir outflow sites also had lower interannual variability in TP yields. The mass balance approach confirmed net N losses in reservoirs, suggesting denitrification of agricultural N, or N burial in sediments. Net retention of P ranged more widely, and multiple systems showed net P export, providing new evidence that legacy P within reservoir systems may mobilize over the long-term. Our results indicate that reservoirs broadly influence the downstream transport of N and P through agricultural river networks, including networks where natural lakes and wetlands are relatively scarce. This calls for a more complete understanding of agricultural reservoirs as open, connected features of river networks where biogeochemical processes are often influential to downstream water quality, but potentially sensitive to changes associated with sedimentation, eutrophication, infrastructure aging, and reservoir management.