Flanked by sandy beaches, Cape Upstart is an imposing granite headland covered in a range of vegetation types from vine thicket to heath. Significant areas of beach scrub and coastal dunes are also protected in the park. The surrounding waters are part of the Great Barrier Reef Marine Park. An important meeting place—the landscapes of Cape Upstart National Park hold deep cultural significance to the Juru people.

Spanning 8,480ha Cape Upstart is made up of three sections—Cape massif, Camp Island and Worungu Bay. The landscapes and seascapes support a variety of important nesting and feeding habitats for species of conservation significance such as turtles and dugong Dugong dugon.

The prominent feature of Cape massif consists of a highly folded 700m high multi-peaked rugged granite massif. Gorges and creek systems crisscross the massif forming a complex north-south range containing diverse ecosystems—a mix of spinifex woodland, heath, beach scrub and rainforest. The park protects one of the largest populations of the endangered northern quoll Dasyurus hallucatus in Australia.

Worungu Bay situated north of the mouth of the Elliott River is a landscape composed of coastal dune systems. Featuring Casuarina foredune plant communities, beach scrub of national significance, areas of salt couch, samphire tidal flats and mangroves.

Camp Island protects endangered microphyll vine forest (beach scrub), a regional ecosystem of concern.