Urbanization and land claim trends for agriculture have led to land use/land cover (LULC) changes, acting as driving forces for several natural environment alterations. The ecosystem services (ES) concept links ecosystem degradation with direct adverse effects on human welfare, emphasizing the importance of balancing human activities and ecosystem health. LULC changes and their impacts on ES are crucial for nature conservation and decision-making. To support sustainable management, a historical (75-year) assessment of Nestos Delta lagoons was conducted, using aerial photos and satellite images, providing valuable insights into the drivers and trends of these changes. Until 1960, water-related Biomes were affected the most, in favor of agricultural (Nestos River incubation) and urban ones, but anthropogenic activities development rate reduced after land reclamation. Since their inclusion in the Natura 2000 network and designation as a National Park, they have been protected from rapid development. Over the past two decades, they have increased the economic value of their cultural ES, while deteriorating regulating and having a minimal impact on provisioning services, resulting in a cumulative loss exceeding USD 30 million during the study period. This study strongly indicates the vital importance of legislative protection and the integration of the ES approach in priority habitat management.