In the present study, a morphological model based on the main governing processes of inlet channels was developed for application in long-term simulations, requiring minimum data on forcing and only key information on the inlet geometry. The model considers the balance between the inlet sand transport due to tides and river flows and the longshore transport due to breaking waves. The resulting equations were numerically implemented and validated first through schematic simulations and then through an application to a real inlet. For the schematic simulations, the sediment transport rates in the inlet and alongshore were maintained constant and the behavior during evolution towards equilibrium was investigated and qualitatively assessed. Then, the model was applied to Mundaú Lagoon inlet (Brazil), a natural inlet sheltered by reefs and with a marked seasonality in river runoff. Thus, the model performance was validated for a complex setting over time scales of decades through comparisons with the observed inlet evolution determined from satellite images. The calculated results of inlet channel morphological evolution exhibited satisfactory agreement with observations. The computational efforts were low making the model suitable for long-term simulations where many alternative scenarios may be explored in a probabilistic manner. In conclusion, the developed model yielded robust and reliable simulation results having the potential for use in the assessment of long-term inlet channel evolution.