A simulation study using the Seasonal Analysis program of the Decision Support Systems for Agrotechnology Transfer (DSSAT 3.5) suite of models was conducted from 2001 to 2003 under a subhumid subtropical climate. The models CERES-Rice and CERES-Wheat in DSSAT 3.5 were calibrated and validated for transplanted rice, direct seeded rice and wheat crops using the soil and weather parameters of Kharagpur, West Bengal, India. The weather generator program, SIMMETEO, was used to generate future weather scenarios based on weather data from 9 consecutive years. These weather scenarios were used in the seasonal analysis program to run each treatment combination with 20 replications. The results of both biophysical and economic analyses of the Seasonal Analysis program predicted an application of 120 kg N/ha along with both rice and wheat crop residues at 4 t/ha for rice, whereas the economical analysis, specifically the Mean-Gini analysis, showed that application of 80 kg N/ha along with both rice and wheat crop residue incorporation at 4 t/ha as the most dominant management options for wheat. The present study revealed that the generated future weather data were reliable and DSSAT could successfully use it to predict the future crop yields under different management practices and select the best one for sustainable production of rice and wheat crops by DSSAT.