Bermagui River estuary has a waterway size (including saltmarsh areas) of 2.2 km2 and a catchment area of 83.5 km2. Majority of the catchment is forested with 41% in NPWS estate (Biamanga National Park and Bermagui Nature Reserve) and 4.6% in Bermagui State Forest. Large areas of the catchment have been subjected to forestry operations with approximately 26% of the catchment cleared for agricultural grazing/rural residential uses. The area of urban development in comparison is minor, representing approximately 2% of the catchment area situated around the lower estuary.
The estuary is primarily used for recreation with waterway uses including recreational boating, fishing, kayaking and swimming while commercial uses oyster aquaculture and the Bermagui boat harbor and marina operations. Bermagui River is a recreational fishing haven with all commercial fishing now prohibited.
Bermagui River is a semi-mature, wave-dominated, barrier estuary that is permanently open to the ocean. The ocean entrance is trained by rock breakwaters on either side with access to Bermagui boat harbour provided from the main channel just inside the river mouth. Historically, the entrance has only required dredging at infrequent intervals because the natural hydrodynamic characteristics of the estuary limit shoaling. Being permanently open to the ocean, the estuary is subject to high level of tidal flushing and characterised by high water clarity.