Marine ecosystems, particularly in coastal regions, are increasingly shaped by human activities occurring both on land and at sea. As anthropogenic pressures intensify, understanding species habitat preferences and their interactions with human-altered environments is critical for guiding conservation efforts. This study provides the first comprehensive assessment of bottlenose dolphin (Tursiops truncatus) habitat suitability and exposure to human activities in Maltese waters, a region characterised by intense maritime activity but limited research effort and baseline knowledge on the species. Using a MaxEnt model, we integrated sightings from multiple surveys (2012–2021) with key environmental (salinity, chlorophyll-a, depth) and anthropogenic (vessel traffic density) predictors to identify areas of ecological importance and potential conflict. Results revealed a strong preference for shallow coastal waters, primarily over the Malta Plateau. Salinity and chlorophyll-a emerged as the strongest environmental drivers, while vessel traffic density had limited standalone influence, possibly reflecting dolphins' behavioural adaptability in resource-rich but human-impacted environments. An exposure index was developed to identify areas where high habitat suitability overlaps with vessel traffic and Fish Aggregating Device (FAD) deployment, highlighting several zones of potential spatial conflict. These findings highlight the importance of integrating ecological and anthropogenic factors to identify high-risk areas and inform more effective conservation strategies for bottlenose dolphins in Malta's coastal waters.