The reported study was undertaken in a small agricultural watershed, namely, Kapgari in Eastern India having a drainage area of 973 ha. The watershed was subdivided into three sub-watersheds on the basis of drainage network and land topography. An attempt was made to relate the continuously monitored runoff data from the sub-watersheds and the whole-watershed with the rainfall and temperature data using the artificial neural network (ANN) technique. The reported study also evaluated the bias in the prediction of daily runoff with shorter length of training data set using different resampling techniques with the ANN modeling. A 10-fold cross-validation (CV) technique was used to find the optimum number of hidden neurons in the hidden layer and to avoid neural network over-fitting during the training process for shorter length of data. The results illustrated that the ANN models developed with shorter length of training data set avoid neural network over-fitting during the training process, using a 10-fold CV method. Moreover, the biasness was investigated using the bootstrap resampling technique based ANN (BANN) for short length of training data set. In comparison with the 10-fold CV technique, the BANN is more efficient in solving the problems of the over-fitting and under-fitting during training of models for shorter length of data set.