Developing countries in the technological transition period seek fast economic growth and give environmental issues lower priority. This is one of the causes of environmental degradation in coastal zones. The Patos Lagoon Estuary, located along the southern coast of Brazil, has accumulated environmental liabilities over the last 30 years due to socioeconomic activities in the city of Rio Grande. These liabilities are particularly conspicuous in the shallow estuarine embayments, which are considered vital habitats due to their high productivity and significance as nurseries (shelter and feeding) for the local biota. Since the 1970s, these habitats have suffered various stressors from uncontrolled urban and industrial expansion, which are responsible for landfills at the estuary shores and the enrichment of the water with nutrients and metals from the disposal of effluents. In the medium to long term, these problems tend to be aggravated by existing projects and policies of industrial and port expansion. One of the most productive environments in this estuary is Mangueira Bay, an oval semi-enclosed bay located south of the city with an area of 23 km2 and a depth mostly below 1.5 m. This embayment is currently a focus of land/water use conflicts involving several social actors, including fishermen, socially excluded people, high-class housing users, public institutions, industries and the general population. In this context, finding a solution that is appropriate and compatible with all social demands on the environmental goods and services provided by the estuary is a difficult task. The process must begin with a technical diagnosis that is extensive and detailed enough to include social, economic and environmental issues. This paper describes the use conflicts of Mangueira Bay and suggests guidelines for a collective management plan.