The economic activities at the South Brazilian Shelf (SBS) are concentrated on the coast causing several impacts. To reconcile biodiversity and habitat conservation in the coastal and marine areas with human activities it is important to identify those sectors and pressures. We conducted an analysis to assess ecosystem risks from multiple drivers and pressures in the continental shelf that extends from the Southernmost point of Brazil (Chuí) to Cabo Frio cape, in Rio de Janeiro State. We used the Integrated Ecosystem Assessment (IEA) methodology, a framework for implementing ecosystem-based management grounded on five steps: scoping, indicator development, ecosystem assessment, risk analysis, and management strategy evaluation. This work developed the scoping step consisting of an assessment tracing sector–pressure–ecological component pressure pathways. Subsequently, links were scored regarding their level of overlap on each ecosystem component, frequency and degree of impact, estimating the magnitude of impact risk of each one of the sectors. The assessment was done involving 20 experts from several backgrounds. In order to validate the results, a literature review was conducted and further discussion with relevant stakeholders took place. As a result, 16 sectors and 19 pressures were assessed to impact 18 ecological components. Fishing, land-based industry, tourism and recreation, the lack of wastewater treatment and coastal infrastructure represented the main economic sectors impacting the area. The major associated pressures were the incidental catch of species, the introduction of contaminants and organic matter into the water, and the generation of waste. The most affected ecosystems, in turn, were those located closer to the coast, such as mangroves, saltmarshes and rocky reefs while the preeminent impacted taxonomic groups were the elasmobranchs, seabirds, reptiles, mammals and bony fish. The literature review corroborated the scenario projected by the experts and the stakeholders’ workshop endorsed the results found. The methodology indicated the most relevant pressures caused by human activities, with more significant impacts related to activities closest to the coastline. Also, it draws attention to the need for the elaboration of public policies that contemplate and support impact reduction of the most important sectors, identifying the priorities for coastal and marine management.