The cemetery is located on the western shore of the upper reaches of Wagonga Inlet, on the point that separates Brice’s Bay from the larger water body. Access is via a moderately steep bush track that joins Wagonga Scenic Drive approximately half a kilometre away. 
The site is owned by the Mt Dromedary Uniting Church Parish.

At the same time as the Free Selection Act came into force (1861) Nerrigundah residents commissioned William Carruthers to survey and construct a road to Wagonga Inlet as an alternative route to the coast at Moruya. Carruthers completed the road in 1862 and a small settlement, known as Wagonga, began to develop at the head of the inlet. 

Population growth was slow but the inlet fulfilled a vital function as a timber shipping centre with a large number of sawmills there over an 87-year stretch beginning with Henry Wither's mill in 1877. 

There were about 200 residents in the area in 1866 finding work in farming, timber getting and gold mining. Alluvial gold was found in the creeks draining Mt Dromedary and in 1892 a large gold bearing reef was discovered close to Punkalla Post Office. Gold was also dredged from Punkalla Creek from 1902. 

A Wesleyan church was completed in 1866 adjacent to the site of the present cemetery and remained in service until the mid 1870s. The cemetery also includes some Anglican burials. 

Over the years the site had become terribly overgrown. In 2010 the Narooma Historical Society instigated a clearing of the site, and began compiling the list of burials with the aim of erecting a plaque commemorating them. 

The cemetery is listed in the heritage schedule (Schedule 5) of the Eurobodalla Shire Council Local Environment Plan as a place of local significance.  In keeping with the requirements of that listing, the Narooma Historical Society compiled a Plan of Management for the site. In partnership with the Uniting Church a Friends of Wagonga Cemetery group was created to provide regular maintenance of the cemetery.

In October 2015 the Narooma Historical Society, with financial support from the Eurobodalla Shire Council, purchased a commemorative plaque. Through the generosity of Friends member Bill Dudley a monument was erected on the site. A dedication ceremony took place on 11 February 2016.