A module that uses neural networks was developed for forecasting the groundwater changes in an aquifer. A modified standard Feedforward Neural Network (FNN), trained with the Levenberg–Marquardt (LM) algorithm with five input variables (precipitation, temperature, runoff, groundwater level and specific yield) with a deterministic component, is used. The deterministic component links precipitation with the seasonal recharge of the aquifer and projects the seasonal average precipitations. A new algorithm is applied to forecast the groundwater level changes in Messara Valley, Crete, Greece, where groundwater level has been steadily decreasing due to overexploitation during the last 20 years. Results from the new algorithm show that the introduction of specific yield improved the groundwater level forecasting marginally but the linearly projected precipitation component drastically increased the window of forecasting up to 30 months, equivalent to five biannual time-steps.