Bivalves are important components of freshwater ecosystems; however, they are also one of the most threatened animal groups, especially members of the order Unionida. The main threats to freshwater bivalves are habitat modification and invasive species. Protected areas are a common way to minimize impacts and preserve native species, but they are rarely designated with a focus on freshwater invertebrates. The main goal of this article was to describe the distribution of freshwater bivalves in the state of Rio de Janeiro, and the relationship between these species and bioclimatic areas, land use and protected areas. Five native and two invasive bivalve species have been reported in Rio de Janeiro. They occur mainly in bioclimatic areas related to the Paraíba do Sul River and Campista Lowlands. The few records of bivalves inside protected areas are in areas of sustainable use that offer a lower level of protection, and frequently in sympatry with invasive bivalves. Thus, the established protected areas in Rio de Janeiro are not adequately effective for freshwater bivalve conservation, and some species remain under threat even within them. Freshwater bivalves thus remain largely unprotected in the state. The development of new protected areas and management plans should consider other faunal groups that are usually ignored, such as freshwater bivalves, to achieve more inclusive and effective protection.