A CELTHYM(CEll-based Long-term HYdrologic Model), a pre-processor and a post-processor that can be integrated with geographic information system(GIS) were developed to predict the stream flow from the small agricultural watershed on the daily basis. The CELTHYM calculates the direct runoff from a grid using SCS curve number method and then sum up all of cells with respect to a sub-catchment area belonged to a stream grid and integrated to an outlet. Base flow of a watershed outlet was computed by integrating of the base flow of each stream grid that was averaged the sub-catchment deep-percolation and calculated with the release rate. Two kind of water budget equation were used to compute the water balance in a grid that was classified into not paddy field and paddy field. One of the two equation is a soil water balance equation to account the soil moisture of the upland, forest and excluding paddy field grid. The other is a paddy water balance equation for the paddy field, calculating the ponding depth, the effective rainfall, the deep percolation and the evapotranspiration.