It preserves an isolated fragment of the Atlantic Forest biome, with semi-deciduous riparian vegetation.

A 2002 federal decree said the name of a conservation unit should where possible be based on its most significant natural feature or its oldest name, so it became the Estação Ecológica Mata do Jacaré by state decree 53.237 of 20 July 2012.

[2] The unit lies along the south shore of the reservoir formed by the Santana Dam on the Jacaré-Guaçu River, which separates the municipalities of Brotas and São Carlos.

[3] The area is hilly and includes steep slopes susceptible to erosion.

[5] An extension of protection around the area has been proposed both to conserve biodiversity and to maintain the water quality of the reservoir.