Stilbaai was declared a marine protected area in 2008. It connects to the land-based Geelkrans Nature Reserve, which ensures that the coastal zone is well protected.

The area, managed by CapeNature, is protected to rebuild overexploited marine life, particularly reef/line fish. It also prevents habitat degradation and preserves the ancient intertidal stonewall visvywers (fish traps), which are archaeologically and culturally important.

Fishing is still allowed in controlled areas, but it is banned in Geelkrans, Skulpiesbaai and the Goukou estuary. Goukou was the first estuary to be included in a marine protected area in the Western Cape.

Stilbaai is a biodiverse area, with a variety of coastal habitats, including dunes, sandy beach, rocky shore, coastal fynbos, salt marshes, reefs and estuarine reeds. These habitats are monitored through various projects to help CapeNature understand the area and plan its activities accordingly.