Marine Protected Areas (MPAs) are essential for preserving marine biodiversity, yet they face challenges from various human pressures, including vessel activities. This study applies a cumulative, normalized vessel density approach across multiple habitat types to examine the impact of maritime activities on the Southwest Marine Protected Area (MPA) in Malta, known as MT101. Vessel activities, including anchoring, mooring, and discharge, pose significant threats to benthic habitats such as sandbanks and seagrass meadows. Despite protective measures, vessels continue to frequent these MPAs, raising concerns about habitat degradation. Using data spanning from 2017 to 2022, this research analyses vessel density distribution and its implications for marine habitats within MPA MT101. The results show the cumulative vessel presence, with passenger and fishing vessels showing consistent high presence along bay areas, and on sensitive habitats such as Posidonia meadows and reefs. While the ecological effects have not been directly measured here, the analysis highlights spatial and temporal hotspots where pressures are likely to be most pronounced, offering a basis for targeted management and monitoring. Proposed mitigation measures include enhanced enforcement of MPA regulations and habitat-specific management strategies. By integrating vessel activity patterns with habitat distribution, this methodological framework provides a transferable tool for assessing cumulative pressures and has direct policy relevance for marine spatial planning and targeted MPA management. The findings emphasize the importance of collaborative efforts among stakeholders to ensure the long-term sustainability of marine ecosystems within MPA MT101. This study contributes valuable insights into the understanding of vessel impacts on MPAs and provides guidance for conservation and management strategies in similar marine environments globally.