Knowledge of the difficulties, costs, and territorial issues surrounding fishing communities seems crucial to achieve sustainable development goals in marine and coastal zones. However, such knowledge is not always available, sufficient, or even identifiable. The seabob-shrimp small-scale fisheries in the shallow waters of the State of São Paulo, in Southeastern Brazil, plays an important role in coastal livelihoods, providing social and economic benefits for a number of local communities and a premium source of regional seafood. Around 4000 fish-workers produce supplies for restaurants, fishmongers and supermarkets in coastal towns with about 2 million inhabitants. Nevertheless, harbor and naval mooring, the construction of pipelines, sewage disposal, controversial seasonal closures, and marine spatial zoning have all restricted the activity. A territorial approach is here proposed to examine the timeline of vertically implemented laws/regulations that may have resulted in a decrease of territories formerly available to that fisheries, accompanied by a comprehensive outlook of the overall policy context. The shrinkage of fishing territories has been evidenced and the kind of territorial loss detected does not seem to be implicit in cost analysis of fisheries, ecosystem services, or compensation. Top-down policies and a misunderstanding of environmental mitigation programs appear to have been contributing to increasing conflicts, mining multi-stakeholder processes and social justice in contrast to the ascendant economic growth of both the oil and gas and port industries. While economic and political pressures seem to shape current fishing territories, the recognition of the diversity of interests and power asymmetries in coastal zones directs our attention to a vital, often ignored, dimension of social reality. Institutional challenges and recommendations, such as territorial use rights and legal innovations are discussed, adding value to the self-organization of local communities for an effective process of balanced power both within and outside legal marine protected areas.