A study of the changes in natural phytodiversity that can be linked to recreational activities on tertiary dunes (grey dunes) is presented. Ten neighboring areas on the Islands of Wolin (Poland) and Usedom (Germany), representing all major disturbance factors (holiday resorts, campgrounds, parking), were chosen with two appropriate reference areas from Usedom and Wolin Island (Poland) that are situated in remote parts of the coast and showed no permanent signs of human disturbance. The results of recreational activities, especially trampling, eutrophication, and the neighboring effects of nearby gardens, parks, or fallow land, were assumed to be the main factors influencing natural dunal phytodiversity. Mechanical stress from trampling could result in a decrease in phytodiversity, whereas rising nutrient levels (e.g., fecal deposits), as well as neighboring effects from urban development and a growing species pool, could lead to an increase in diversity, including the occurrence of generalist or ruderal species not typical of unmodified dunes. Hence, changes within natural dunal phytodiversity depend on character and intensity of recreational activities. Results show that the location of the beach largely influences visitor numbers and hence the level of disturbance. At holiday resorts, damage to dunes can be low, even though tourist numbers on the beach are very high, if the dunes can be overlooked from the main promenade. Visitors are reluctant to trespass onto the dunes if they are being watched by many people. Nevertheless, areas without major signs of human disturbance were mostly found on remote dunes that were only accessible by foot or bicycle. Application of established phytodiversity indices (e.g., H′) showed drawbacks in detecting the different types of disturbance; however, sensitivity is improved by a modified index (H′_dune).