Property rights are important institutions for regulating the use of valuable natural resources from coastal ecosystems. In this case study, we identify and analyze property rights and user patterns related to small-scale coastal fisheries in the Stockholm Archipelago, Sweden. User patterns and user groups have changed significantly over the last century, as commercial fishing has been increasingly replaced by recreational activities. Interviews with local resource users and owners of water properties in two different areas, Möja and Ornö parishes within the Stockholm Archipelago, revealed a very diverse pattern of property and user rights, with a large number of water and fishing rights owners. Recreational fisheries, including both sport and household fishing, seem to predominate in both areas, but ownership differs. In Möja, most waters are collectively owned, whereas in Ornö, individual ownership predominates. Very few examples of local influence on fisheries management were found in either area, although the social structure for joint management does exist in Möja. Instead, larger-scale institutions at the regional, national, or international level regulate fisheries, often not addressing local conditions and fish populations. The ongoing shift in resource use has created a heterogeneous user group, and the limitations of centralized management authorities in dealing with the diversity in the coastal ecosystem have created mismatches within the social–ecological system. Combined with a large-scale decline in coastal fish stocks, these mismatches challenge the existing local property rights arrangements as well as the more centralized regulatory management structure. A key issue for fisheries management is how to develop and stimulate appropriate distribution of management functions at different geographical scales and organizational levels. The complexity and diversity in archipelago fisheries call for multilevel arrangements and cross-scale coordination, and initiatives have been taken by both central governmental authorities and local user groups to collaborate concerning habitat restoration and protection of important spawning grounds.