Abstract: Missing data in water resources studies prevent planning. For this reason, data estimation studies are carried out. In this study, ANFIS (Adaptive Neural Fuzzy Inference System) was used to complete the missing data. At the study area, the Yesilirmak Basin located in the north of Turkey, input variables from seven stations and output variable from one station were determined. In the research, 80% (378 months of data) of 504 months of the flow data between 1969 and 2011 was used in the training phase and 20% (126 months of data) was employed in the testing one. The decision tree was used instead of the trial and error method in the selection of input variables and determining the number of membership functions in ANFIS models. It was concluded that the ANFIS model established with the information obtained from the decision tree is successful compared to the randomly established ANFIS models. Using the decision tree before ANFIS models are created will not only minimize the time spent on the model development, but also prevent the best of the possible models from being overlooked.