In the final segment of the geographical unit named Lower Middle Course of the Paraíba do Sul River (Ab Saber, 1958), located in the Fluminense area of the state of Rio de Janeiro, there is a subunit named Domain of the River Islands, which has well-preserved biodiversity when compared to the more developed areas in the states of Rio de Janeiro and São Paulo found upstream. With the exception of the Domain of the Mountain Ranges and Plateau, in the Upper Valley of the Paraíba do Sul River, the upstream areas have been degraded especially in the highly developed areas in the states of Rio de Janeiro and São Paulo, due to their elevated population and industrial densities (COELHO, 2012; ICMBio, 2011). The sprawl translates into industrial and household pollution, large deforested areas, harmful effects on the aquatic biota caused by the proliferation of dams, erosion, sedimentation, introduction of alien species and toxic leaks (ARAUJO, 2004; ARAUJO et al., 2005). Although these factors originating in border waters also threaten the River Islands, the area was recognized as a strategic location by the Chico Mendes Institute for Biodiversity (ICMBio, 2011) due to its rich biodiversity (BIZERRIL, 2001) and a number of endangered species found in the area (CARAMASCHI et al, 1991; BIZERRIL, 2001). This Institute shall enforce the actions established by the National System of Conservation Units, foster, and carry out programs of research, protection, conservation and preservation of the biodiversity, and exercise the power of environmental police in the federal Conservation Units. Existing surveys on the occupation of the Paraíba do Sul Basin are of particular interest to this study, including those pertaining to the Domain of the River Islands region, the importance of local fish species for the riparian communities, the ecologic interactions between river systems, the environmental, spatial, physic and biological characteristics of this area of the Paraíba do Sul River, as well as other scientific studies. The aim of this dissertation is to collect data by reviewing existing literature and experiences gathered in the field, in order to pool information and present reflections on how the river segment of Domain of the River Islands is able to maintain, within the polluted and degraded Paraíba do Sul Basin, a relatively well-preserved ecosystem, which therefore must be protected.