Nitrate released from a variety of land-use activities is a major factor in the degrading conditions observed in many watersheds and estuaries. In this research a spatially lumped model is developed to estimate annual nitrate loads and concentrations from over 100 small watersheds in the Canadian province of Prince Edward Island (PEI). Nitrate source concentrations are associated with major land-use categories, and nitrate attenuation, based on the width of riparian zones, and transport delay due to groundwater residence time are simulated. To investigate the uncertainty of the results, model parameters were selected using a Latin hypercube sampling method. Nitrate concentrations from 12 watersheds were used for model calibration (R2 = 0.91), while 118 other watersheds were used for verification purposes (R2 = 0.82). Overall, the lumped parameter model is shown to be a useful tool for simulating annual nitrate loadings from agricultural watersheds when detailed spatiotemporal agricultural land-use data are available. For PEI the model results indicate that nitrate loadings to estuaries are strongly related to agricultural land, especially the land area in potato production.