We applied multilayer perceptron (MLP) and radial basis function (RBF) neural network in upstream and downstream water quality stations of the Karaj Reservoir in Iran. For both neural networks, inputs were pH, turbidity, temperature, chlorophyll-a, biochemical oxygen demand (BOD) and nitrate, and the output was dissolved oxygen (DO). We used an MLP neural network with two hidden layers, for upstream station 15 and 33 neurons in the first and second layers respectively, and for the downstream station, 16 and 21 neurons in the first and second hidden layer were used which had minimum amount of errors. For learning process 6-fold cross validation were applied to avoid over fitting. The best results acquired from RBF model, in which the mean bias error (MBE) and root mean squared error (RMSE) were 0.063 and 0.10 for the upstream station. The MBE and RSME were 0.0126 and 0.099 for the downstream station. The coefficient of determination ($R^2$) between the observed data and the predicted data for upstream and downstream stations in the MLP was 0.801 and 0.904, respectively, and in the RBF network were 0.962 and 0.97, respectively. The MLP neural network had acceptable results; however, the results of RBF network were more accurate. A sensitivity analysis for the MLP neural network indicated that temperature was the first parameter, pH the second and nitrate was the last factor affecting the prediction of DO concentrations. The results proved the workability and accuracy of the RBF model in the prediction of the DO.