Water availability is essential for the appropriate analysis of its sustainable management. We performed a comparative study of six hydrological balance models (Témez, ABCD, GR2M, AWBM, GUO-5p, and Thornthwaite-Mather) in several basins with different climatic conditions within Spain in the 1977–2010 period. We applied six statistical indices to compare the results of the models: the Akaike information criterion (AIC), the Bayesian information criterion (BIC), Nash–Sutcliffe model efficiency coefficient (NSE), coefficient of determination (R2), percent bias (PBIAS), and the relative error between observed and simulated run-off volumes (REV). Furthermore, we applied the FITEVAL software to determine the uncertainty of the model. The results show that when the catchments are more humid the obtained results are better. The GR2M model gave the best fit in peninsular Spain in a UNEP aridity index framework above 1, and NSE values above 0.75 in a 95% confidence interval classify GR2M as very good for humid watersheds. The use of REV is also a key index in the assessment of the margin of error. Flow duration curves show good performance in the probabilities of exceedance lower than 80% in wet watersheds and deviations in low streamflows account for less than 5% of the total streamflow.