Outflow from agricultural fields carries diffuse pollutants like nutrients, pesticides, herbicides etc and transports the pollutants into the nearby streams. It is a matter of serious concern for water managers and environmental researchers. The chemical characteristics of applied chemical, percentage of area under the chemical application etc are some of the main inputs that cause pollution concentration as output in streams. Each of these inputs and outputs may contain measurement errors. Fuzzy rule based model based on fuzzy sets suits to address uncertainties in inputs by incorporating overlapping membership functions for each of inputs even for limited data availability situations. In this study, the property of fuzzy sets to address the uncertainty in input-output relationship is utilized to obtain the estimate of concentrations of a herbicide, atrazine, in a stream.