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Effective management of dairy manure is important to minimize N losses from cropping systems, maximize profitability, and enhance environmental sustainability. The objectives of this study were (i) to calibrate and validate the DeNitrification-DeComposition (DNDC) model using measurements of silage corn (Zea mays L.) biomass, N uptake, soil temperature, tile drain flow, NO3- leaching, N2O emissions, and soil mineral N in eastern Canada, and (ii) to investigate the long-term impacts of manure management under climate variability. The treatments investigated included a zero-fertilizer control, inorganic fertilizer, and dairy manure amendments (raw and digested). The DNDC model overall demonstrated statistically "good" performance when simulating silage corn yield and N uptake based on normalized RMSE (nRMSE) < 10%, index of agreement (d) > 0.9, and Nash-Sutcliffe efficiency (NSE) > 0.5. In addition, DNDC, with its inclusion of a tile drainage mechanism, demonstrated "good" predictions for cumulative drainage (nRMSE < 20%, d > 0.8, and NSE > 0.5). The model did, however, underestimate daily drainage flux during spring thaw for both organic and inorganic amendments. This was attributed to an underestimation of soil temperature and soil water under frequent soil freezing and thawing during the 2013-2014 overwinter period. Long-term simulations under climate variability indicated that spring applied manure resulted in less NO3-leaching and N2O emissions than fall application when manure rates were managed based on crop N requirements. Overall, this study helped highlight the challenges in discerning the short-term climate interactions on fertilizer-induced N losses compared with the long-term dynamics under climate variability.