Excess nitrate concentration leads to excessive algal growth that reduces dissolved oxygen for aquatic animals. A significant strategy to preserve the water quality of aquatic systems is through nitrate level assessment. However, use of nitrate sensors and existing laboratory approach is costly and requires a huge effort. This study investigated the application of computational intelligence for measurement of nitrate concentration in a tilapia fishpond at Rizal province, Philippines, based on physico-limnological parameters such as temperature, electrical conductivity, and pH level. Artificial neural network (ANN) algorithms including feed-forward (FNN) and recurrent (RNN) neural networks were developed and optimized using genetic algorithm (GA) to improve their predicting performances. Genetic programming (GP), through GPTIPSv2 tool, was configured to generate a fitness function. This function is the principal component of GA optimization to produce optimal number of hidden neurons for ANN architecture that resulted in 2 neurons for GA-FNN and combination of 92, 31, and 11 neurons for each hidden layer using the GA-RNN model. Based on evaluation results, all models provided acceptable results with error and predictive accuracy values approaching 0 and 1, respectively. However, the GA-FNN model outperformed other models with 3.26 RMSE, 2.23 MAE, and 0.97 R2 values which proved to be the most effective and suitable model for the indirect measurement of nitrate concentration.