Coastal areas are at the centre of human–nature relationship, shaped by recreation, tourism and aesthetic values. However, socioeconomic drivers of biodiversity change in coastal areas have received less attention. Soft sediment seafloors support diverse species communities and contribute to ecosystem functionality. One of the main threats is dredging, which sweeps resident organisms. Dredgings are commonly done to deepen waterways, but also for the purposes of private housing. The ecological impacts of these small‐sized dredgings are not well known over broad environmental and geographical gradients. We developed a simple approach for spatial integration of ecological and socioeconomic system, to describe how recreational land use change contributes to the loss of marine biodiversity. It shows how human behaviour, such as preference for a location of second home, can be derived from spatial data and coupled with ecological change. We characterize typical locations of second homes based on accessibility, aesthetics and environment, and with the information identified suitable areas for new second homes. We also quantified typical areas of dredging, based on the depth and substrate of the sea floor, and the extent of the reed beds, influencing the access to properties. We then simulate an annual increase of new second homes and expected land‐use change, namely dredging of shores. Finally, we quantified the realized and projected loss of marine biodiversity from dredged sites, based on species distribution models, relying on extensive ecological data collected from over 170,000 underwater sites. We found that small‐sized dredging can be detrimental to coastal biodiversity, as dredging targets shallow, photic bays and lagoons, with diverse algal and aquatic plant communities, with limited recovery potential. Dredgings also had broad impacts on benthic faunal habitats, which maintain ecosystem processes and functions. Our results reveal a significant ecological change driven by recreational land use. Reversing the trend of biodiversity loss requires a holistic understanding of socioecological systems. Our results highlight the need for integrating land–sea interactions into conservation policies and reforming current land‐use regulation for the benefit of marine biodiversity. Read the free Plain Language Summary for this article on the Journal blog.