São João River
- Igarapé São João
- São João Grande River
- São João Pequeno River
- São João River (Canoas River tributary)
- São João River (Cubatão River tributary)
- São João River (Dos Patos River tributary)
- São João River (Iguazu River tributary)
- São João River (Ji-Paraná River tributary)
- São João River (Mato Grosso do Sul)
- São João River (Mato Grosso)
- São João River (Minas Gerais)
- São João River (Negro River tributary)
- São João River (Paraná River tributary)
- São João River (Pernambuco)
- São João River (Pitangui River tributary)
- São João River (Rio de Janeiro)
- São João Surrá River
- São João da Barra River
- São João de Meriti River
- São João do Paraíso River