Pollutant load reductions are often required to restore aquatic ecosystems experiencing eutrophication. Loads can be estimated using watershed models or data from monitoring stations, however data availability can limit the timeliness or comprehensiveness of the load estimates. We developed an approach to address this challenge that used watershed model results to estimate the proportion of annual nonpoint source nitrogen (N), phosphorus (P) and sediment (Sed) loads derived from unmonitored catchments. This proportion was multiplied by the nonpoint portion of United States Geological Survey (USGS) estimated annual river loads to account for annual variation in hydrologic conditions. Total loads were calculated as the sum of measured river loads, reported point sources from unmonitored areas and the estimated nonpoint source loads from unmonitored catchments. We applied this approach to the Chesapeake Bay because of its socio-economic and ecological importance. Median watershed loads for N, P and Sed were 140, 6.4 and 3030 Mg year−1, respectively (1990–2004). Nonpoint source loads from the monitored areas constituted the greatest source of N, P and Sed (55, 47 and 74% respectively) to the Bay. The high N, P and Sed yield rates (7.3, 0.38 and 99 kg ha−1 year−1, respectively) from nonpoint loads originating from unmonitored areas near the Bay resulted in 25, 32 and 26% (N, P and Sed, respectively) of the Bay's total loads (excluding direct atmospheric deposition, shoreline erosion and oceanic inputs). Disproportionately high loads of P and Seds were associated with years that experienced elevated discharge whereas N loads were directly related to discharge. Error estimates indicated that our methods were most reliable for N (±6%) but reasonable for P (±22%) and provide an effective technique for the timely estimation of pollutant loads from watersheds with unmonitored catchments. Management strategies that decrease N deposition and reduce runoff to control P and Sed transport will effectively reduce pollutant loads. Published in 2010 by John Wiley & Sons, Ltd.