The river is important to crocodile conservation as it provides habitat for Queensland's most dense population of the animal.

It continues east crossing the Bruce Highway then veers south through Melaleuca forests and discharges through estuarine wetlands and mangrove ecosystems[4] into Repulse Bay near Conway Beach and then onto the Coral Sea.

The estuary functions as a result of river energy with a tide dominated delta.

[9] The Proserpine was rated as the river in Queensland where people were most likely to see a saltwater crocodile from 2000 to 2012, with 151 sightings recorded over the period.

[11] According to a survey conducted from 2016 to 2019, the Proserpine River had the highest density of crocodiles in Queensland, with 5.5 per kilometre (3.4 per mile).