The lagoon is located approximately 5 kilometres (3.1 mi) south-east of the town of St Helens. It lies partly on private land and partly at the southern end of the St Helens Point conservation area. One of a chain of wetlands along St Helens Point, it is 200 to 300 metres (660 to 980 ft) inland from the coast, near a dunefield. About 650 metres (2,130 ft) long and 150 metres (490 ft) wide, it is dystrophic, with tannin-stained, low-nutrient, acidic waters. Water levels fluctuate with rainfall and reach a depth of 2 to 3 metres (6 ft 7 in to 9 ft 10 in).
A total of 51 vascular plant species were recorded from the lagoon by a recent study. Of that total, half were species that grow in swamps or damp areas; vegetation common to dry areas, coastal woodland and Melaleuca forest made up the remainder of the list. The lagoon's aquatic flora is equally rich. Several rare species occur there.
Although Jocks Lagoon is listed as a Ramsar Site, it does not meet all four criteria that determine a site as a Ramsar Site. The lagoon does not meet criterion four, which states that a Ramsar Site is one that "supports species at critical stages or provides refuge in adverse conditions."