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Pollutant load estimation is essential for watershed management and water pollution control. For most watersheds, only sparse water quality measurements (e.g. monthly data) are available. The influence of input data on the accuracy of non-point source pollution load estimation is studied using the water quality and stream flow data from a small watershed in Hong Kong. Comparison and analysis of the results using 8 different methods show that the accuracy of stream-flow runoff is the single most important factor for the calculation of pollutant load. Based on the results, the stream flow correction coefficient is advanced to provide a more reliable load estimation. The improved method of pollutant load estimation can be easily applied in practice since the stream-flow runoff can be measured by hydrological station or estimated with various hydrological methods.