Two models were developed to simulate energy flows in a mangrove area of A. germinans and A. bicolor in the Bay of Panama, considering the importance of these areas in CO2 fixation. The first model (black box) consisted of the use of artificial neural networks for estimation, using meteorological data and energy flows calculated by the Eddy Covariance method for model training. The second model (grey box) used the RC circuit theory, considering a non-steady state model for the flow of water from the ground to the atmosphere. A methodology was developed to reduce the uncertainty of the data collected by the sensors in the field. The black box model managed to predict the fluxes of latent heat (R2 > 0.91), sensible heat (R2 > 0.86), CO2 (R2 > 0.88), and the potential of water in the air (R2 > 0.88) satisfactorily, while the grey box model generated R2 values of 0.43 and 0.37, indicating that it requires further analysis regarding the structuring of the equations and parameters used. The application of the methodology to filter the data improved the effectiveness of the model during the predictions, reducing the computational capacity necessary for the resolution of the iterations.