The objective of this paper is to develop the microorganism concentration simulation model for the health related effect analysis while farmers and water managers reuse the wastewater for agricultural irrigation. This model consists of the CE-QUAL-R1 model and the CREAMS-PADDY model. The CE-QUAL-R1 model is the 1-D numerical model to analyze the water quality of the reservoir and the CREAMS-PADDY model is modified from CREAMS model for considering the hydrologic cycles in paddy field. This model was applied to examine the application by the observed data from 2003 in Byoungjum study area. From this research, the average root mean square error (RMSE) for the simulated concentration during the calibration period was 0.51 MPN/100ml and correlation coefficient (R²) was 0.71. And the RMSE for the simulated concentration during the verification period was 0.46 MPN/100ml and R² was 0.73. This simulation results show that the coliform inflow concentrations by the wastewater irrigation wield great influence upon the temporal coliform concentrations in paddy field.