The overloaded nonpoint source (NPS) nutrients in upper streams always result in the nutrient enrichment at lakes and estuaries downstream. As NPS pollution has become a serious environmental concern in watershed management, the information about nutrient output distribution across a watershed has been critical in the designing of regional development policies. But existing watershed evaluation models often encounter difficulties in application because of their complicated structures and strict requirements for the input data. In this paper, a spatially explicit and process-based model, Integrated Grid's Exporting and Delivery model, was introduced to estimate annual instream nutrient levels. Each grid cell in this model was regarded as having potentials of both exporting new nutrients and trapping nutrients passing by. The combined nutrient dynamics of a grid is mainly determined by the grid's features in land use/land cover, soil drainage, and geomorphology. This simple-concept model was tested at some basins in north Georgia in the USA. Stations in one basin were used to calibrate the model. Then an external validation was employed by applying the calibrated model to stations in the other neighbor basins. Model evaluation statistics implied the model's validity and good performance in estimating the annual NPS nutrients' fluxes at the watershed scale. This study also provides a promising prospect that in-stream annual nutrient loads can be accurately estimated from a few public available datasets.