Lake ecosystems are extremely sensitive to nitrogen growth, which leads to water quality degradation and ecosystem health decline. Nitrogen depositions, as one of the main sources of nitrogen in water, are expected to change under future climate change scenarios. However, it remains not clear how nitrogen deposition to lakes respond to future meteorological conditions. In this study, a source-oriented version of Community Multiscale Air Quality (CMAQ) Model was used to estimate nitrogen deposition to 263 lakes in 2013 and under three RCP scenarios (4.5, 6.0 and 8.5) in 2046. Annual total deposition of 58.2 Gg nitrogen was predicted for all lakes, with 23.3 Gg N by wet deposition and 34.9 Gg N by dry deposition. Nitrate and ammonium in aerosol phase are the major forms of wet deposition, while NH3 and HNO3 in gas phase are the major forms of dry deposition. Agriculture emissions contribute to 57% of wet deposition and 44% of dry deposition. Under future meteorological conditions, wet deposition is predicted to increase by 5.5% to 16.4%, while dry deposition would decrease by 0.3% to 13.0%. Changes in wind speed, temperature, relative humidity (RH), and precipitation rates are correlated with dry and wet deposition changes. The predicted changes in deposition to lakes driven by meteorological changes can lead to significant changes in aquatic chemistry and ecosystem functions. Apart from future emission scenarios, different climate scenarios should be considered in future ecosystem health evaluation in response to nitrogen deposition.