Guanabara Bay (GB) is the second largest bay in the coast of Brazil (384 km2) (22o41 to 22o56 S ; 43o02 to 43o18 W). In its surroundings live 16 million inhabitants (6 million in Rio de Janeiro city). This system experiences steep spatial gradient from the entrance to inner bay. GB receives high load of nutrients and organic material from riverine sources and from domestic and industrial sewage inputs. As a consequence, this system is characterized as a high eutrophicate and polluted one. In spite of its poor environmental status, GB still presents many living resources who use the bay as a refuge, feeding and nursery grounds, with some of those species having commercial interest. An important characteristic of GB is the influence of South Atlantic Central Water, a deep, cold and rich nutrient water, that enters the bay during the Cabo Frio upwelling period. This phenomenon permits to maintain the bay at a relative good health level in its central part, in contrast with the marginal areas highly polluted. Although encroached on by urban expansion, the inner east margins of Guanabara Bay is still bordered by a 90 km2 fringing mangrove system, of which 43 km2 is an environmental protection area, Guapimirim.