The conventional methods of application of nitrogen fertilizers might be responsible for the increased nitrate concentration in groundwater of areas dominated by irrigated agriculture. Appropriate water and nutrient management strategies are required to minimize groundwater pollution and to maximize nutrient use efficiency and production. Design and operation of a drip fertigation system requires understanding of nutrient leaching behavior in cases of shallow rooted crops such as potatoes which cannot extract nutrient from a lower soil depth. This study deals with neuro-fuzzy modeling of nitrate (NO3−) leaching from a potato field under a drip fertigation system. In the first part of the study, a two-dimensional solute transport model was used to simulate nitrate leaching from a sandy soil with varying emitter discharge rates and fertilizer doses. The results from the modeling were used to train and validate an adaptive network-based fuzzy inference system (ANFIS) in order to estimate nitrate leaching. Two performance functions, namely mean absolute percentage error (MAPE) and correlation coefficient (R), were used to evaluate the adequacy of the ANFIS. Results showed that ANFIS can accurately simulate HYDRUS-2D behavior regarding nitrate leaching under the circumstances of the present study.