To help manage excess nitrogen in the environment includes streams and avoid unintended consequences, it is important to better understand how land-use, water use, climate and emission changes may modulate the system’s exposures to pollutants and influence managment targets. The biogeochemical processing of nitrogen and associated pollutants is driven by meteorological and hydrological processes in conjunction with pollutant loading. There are feedbacks between meteorology and hydrology that will be affected by land-use change and climate change. Changes in meteorology will affect pollutant deposition. It is important to account for those feedbacks and produce internally consistent simulations of meteorology, hydrology, and pollutant loading to drive the (watershed/water quality) biogeochemical models. In this study, the ecological response to emission reductions in streams in the Potomac watershed were modeled using the linked one comprehensive/environment model, namely the linkage of Community Multiscale Air Quality (CAMQ) model, Weather Research & Forecasting (WRF) model, Variable Infiltration Capacity (VIC) model and Model of Acidification of Groundwater In Catchment (MAGIC) model from 2002 to 2010.The simulated results (such as NO3, SO4, and SBC) fit well to the observed values. The linkage provides a generally accurate, well-tested tool for evaluating sensitivities to varying meteorology and environmental changes on acidification and other biogeochemical processes, with capability to comprehensively explore strategic policy and management design.