A stochastic production function specification is used to value the variability in agricultural productivity of groundwater use in rainfed lowland rice areas by farmers using shallow tube wells (STWs). The study was done in Southern Philippines Province o f Cotabato. Using survey data, this study first estimated the mean rice yield function with the cost of pumping, which represents well depth and water availability, used as water supply proxy variable input into the stochastic production function. The results of the estimated mean yield function showed that machineries cost, cost of pesticides, and cost of pumping are the most important determinants of yield levels of rice grown during wet season cropping. The mean yield function revealed a diminishing marginal productivity for the cost of pumping. Nitrogen fertilizer was found to be positively related to yield in the dry season cropping in the sample study area.