This study is conducted to investigate the relationship between paddy productivity and soil moisture deficit in a selected irrigation scheme in the Intermediate zone of Sri Lanka. The availability of water for crop growth is estimated using a soil moisture balance equation using field data for a period from 2005 to 2014 to find the soil moisture deficit. A regression showed that relationship between paddy productivity and severity of soil moisture deficit in Yala season is not statistically significant. However, the decrease of paddy productivity during Maha season is influenced by both number of days of soil moisture stress and the total soil moisture stress and the results are found to be statistically significant. About 72% and 88% of the variation of paddy productivity can be explained by the total number of days with soil moisture stress and total soil moisture stress respectively.