The caves and their surrounding forest area are protected by the almost 1,800-acre Aguas Buenas Cave and Caverns System Nature Reserve (Spanish: Reserva Natural Sistema de Cuevas y Cavernas de Aguas Buenas) since 2002, which also extends to the municipalities of Caguas and Cidra.
[1][2] The reserve is important for the number of bat species found in the system, some of which are endangered (Mormoops blanvillei, Monophyllus redmani and Pteronotus portoricensis).
[3][4] In addition to being an important bat preserve, the nature reserve protects an important hydrological basin which is the source of a number of rivers and creeks that form part of the Loíza River basin.
[5] The cave system is found in one of the oldest karst zones in Puerto Rico.
[3] Cueva Ermita (Spanish for "hermitage cave"), also known as Cueva Nivel del Rio ("river-level cave"), is the source of the Cagüitas River.