The BASINS model, developed by the United States EPA, is a popular simulation tool for predicting watershed responses, such as runoff, pollution exports, and water quality. It requires large amounts of data to set parameters. Many studies state that model input is a major source of model uncertainty. Thus, improvements to the quality and completeness of the data will improve the certainty of the model. The objective of this study is to discuss the effects of spatial data, including digital elevation models (DEMs) and spatial rainfall records, on predictions of runoff from the BASINS model. The result shows that both DEMs and rainfall data can significantly influence peak flow and runoff volume. Rainfall input has more influence on the curve shape of hydrograph than DEM resolution. DEM resolution can have more impact on peak flow predictions than rainfall input. Because the model uncertainties from DEMs and rainfall records influence each other, the prediction error does not always decrease when DEM resolution increases. The present results show that the BASINS model produces reliable answers in the case area when the grid size is less than 100 m × 100 m and the precipitation records from the Bihu Rainfall Station are correct and complete.