This article addresses the problem of sedimentation at the entrance of a harbour by evaluating and understanding the sediment dynamics in the adjacent beaches. The results of the methodology applied to acknowledge the beaches' sediment dynamics were used to diagnose the problem's cause and to interpret its evolution. The methodology includes analysis of data from a monitoring programme and process-based mathematical modelling of the alongshore and cross-shore beach dynamics. The integration of both allowed the authors to investigate the hydromorphological behaviour of the harbour-adjacent beaches and to conclude that (i) the harbour and adjacent beaches are a single morphological system, and thus require integrated management; (ii) the study area is exposed to a seasonal wave regime, which induces a local sediment transport pattern and consequently the main seasonal morphological characteristics of the study area; and (iii) the process of sand accumulation at the harbour entrance is irreversible without human intervention. Because harbours should be designed and constructed based on two criteria—capacity of depth self-maintenance and integration, with minimum impact on the local morphodynamics—this study highlights the need for monitoring and identifying the total extension of the active beach, particularly in coastal environments with seasonal hydromorphological variations, before deciding on harbour layout relative to the sedimentary littoral transit.