The numerical source-apportionment model is an efficient and useful method for analyzing water-quality responses to nutrient loading in rivers and lakes. In this study, the Environmental Fluid Dynamic Code (EFDC) and numerical source-apportionment model were applied to Lake Bali in Jiujiang City, China to predict the contributions of various pollution sources to the lake at any time and position. We calibrated and validated the model by comparing its predictions with observed hydrodynamic and water-quality parameters from 2014 to 2015. Application of the calibrated model to simulate water-quality responses to a pollution source showed that the contribution of a pollution source to water quality in the lake has strong spatial heterogeneity. The results provide useful information for the optimization of pollution load reduction in Lake Bali and can be used to determine the most effective implementation of its pollution-control plan. The model built in this study can also be used for pollution source-apportionment in other urban lakes and is superior to other traditional source-apportionment models.