Urban expansion is widely acknowledged to have a substantial impact on water bodies. The objective of this work is to propose and apply a composite index to evaluate the quality of Permanent Preservation Areas (PPAs), which protect urban rivers. The PPAWater index aggregates information from six indicators, namely, sanitary sewage, precarious settlement, urban drainage, level of occupation, conservation units, and preservation area, established by the municipal master plan. When applied to sub-basins in the city of Fortaleza, Ceará, the fifth most-populated city in Brazil, the index shows that the localities lacking sufficient sanitation infrastructure and with fewer hectares of protected areas register as the most vulnerable PPAs. The PPAWater index is an important tool to guide urban environmental planning, formulation, and management of public policies for the protection of urban water resources. It can be used by municipal managers to evaluate environmentally sensitive areas.