The Reserve covers approximately 400 km2, including 50 km of coastline, and is located between the mouth of the river Lempa and the Jucuarán mountain range.

The Reserve contains the largest mangrove estuary in El Salvador and includes bays, canals, sandy beaches, islands, forests and a freshwater lagoon complex.

[citation needed] Bahia Jiquilisco is also one of two primary hawksbill sea turtle (Eretmochelys imbricata) nesting habitats in the eastern Pacific Ocean.

In the eastern Pacific Ocean, the species is extremely rare and as recently as 2007 most researchers thought hawksbills had been completely eliminated in this region of the world.

[2] The discovery of hawksbill nesting in Bahia Jiquilisco and in Estero Padre Ramos (Nicaragua) changed the conservation outlook for this imperiled population and has provided renewed hope for recovery.