In this paper, the lumped quasi-distributed hydrological model HEC HMS is used to simulate the rainfall–runoff process of the Mekerra watershed, located in the northwest of Algeria. The model parameters’ uncertainty and the predictive intervals were evaluated with the generalized likelihood uncertainty estimation (GLUE) approach. According to the results, good simulations were obtained with different values of variables for many sets of parameters generated randomly by the Monte Carlo procedure, which is known as Equifinality. After the analysis, only the hydraulic conductivity at saturation parameter appears well defined, taking values within a limited range. In addition, results indicated that combinations of likelihood measures associated with multiple and different periods of observations reduce a posterior uncertainty of estimated parameters and predictive intervals in some degree. Overall, the GLUE analysis showed that there is a significant uncertainty associated with hydrological modelling of watershed Mekerra, to a great extent due to multiple sources of errors.