The Agricultural Policy/Environmental eXtender (APEX) model has been widely used to assess changes in agrochemical loadings in response to conservation and management led by US Department of Agriculture (USDA). However, the existing APEX model is limited in quantification of wetland water quality functions. This study improved the current model capacity to represent wetland water quality functions by addition of a new biogeochemical module into the APEX model. The performance of an enhanced APEX model was tested against five observed outgoing water quality variables (e.g., sediment, organic N, NO3, NH4 and PO4) from a wetland within the Eastern Shore of Maryland. Generalized Likelihood Uncertainty Estimation (GLUE) was implemented to assess model uncertainty. The enhanced APEX model demonstrated that it could effectively represent N and P cycling within the study wetland. Although improvement of model performance was limited, the additions of wetland biogeochemical routines to the APEX model improved our understanding of inner mass exchanges within N and P cycling for the study wetland. Overall, the updated APEX model can provide policymakers and managers with improved means for assessment of benefits delivered by wetland conservation.