[9] The peninsula's cliffs have erosional features caused by wave-cutting, differences in rock types, bedding, and other bedrock characteristics that have led to the formation of caves and notches.

Nelson Bay Cave is located on the south-facing slope of the Robberg Peninsula in quartz-sandstone and quartzite deposits.

The early excavations revealed evidence of pottery, sheep remains, human burials, stone tool artifacts, ochre fragments, and shell ornaments.

[2][10][11] Later excavations in the early 1970-1972  by Inskeep and Richard G. Klein exposed Middle Stone Age deposits and bedrock material, estimated to date to the late Marine Isotope Stage (MIS) 5.

The lower bed of the cave has MSA deposits that occur in sterile gray loam and iron-rich sediments.

On top of GAI lies the pit fill, which has a mixture of debris and cultural material, which is also mixed with loamy sand.

The Wilton industry is characterized by many small convex scrappers, backed tools made of quartz and chalcedony.

[2][6] Tortoise shells occur in the youngest layers of the sequence (Post-climax Wilton) and have been associated with the movement of the cave dwellers and hand-to-hand exchanges.

Bugle lily (Watsonia) corms were amongst the first plant remains found in the cave including the African potato (Hypoxis).

[2][19][12] Other plant material include dwarf eelgrass (Zostera capensis) preserved in a mussel shell and seeds of bully trees (Sideroxylon), Sumac (Rhus), and persimmon (Ebenaceae) family.

Seeds of spurge flower (Jatropha capensis), wild peach (Kiggelaria africana), and mountain maytenus (Mytenus oleoides) were brought in by birds and not attributed to human diets in the cave.

Lastly, there is an abundance of shellfish remains in the top layers of the sequence showing a shift into exploiting coastal resources.

[20]  Fossils of bird species include cape gannet (Morus capensis), albatros (Thalassarche sp.

Those that occur from the early LSA Robberg to the late Holocene Post-climax Wilton industry include Chacma baboons, rock hyrax, bushpig, cape buffalo, southern reedbuck, grysbok, and vaalribbok.

Modern human remains are found during the Middle to Late Holocene units including water mongoose, sea elephant, bushbuck, blue duiker, and dolphins.

Additionally, the cave is located on the coast of the southern Cape and provides insights about the Paleo-Agulhas Plain (PAP).

[22] The coastline moved 100 km seaward, and the sea level dropped to 130 meters during the Last Glacial Maximum.

[25] The faunal remains of Nelson Bay Cave have been used to explain food and resource exploitation during the MSA to LSA transition as they show hunting preferences and dietary shifts.

The Holocene units show a resource exploitation shift where the sequence has marine mammals and an increase in bone tools.

[30] These debates are based on four parts, the chronology and dating of the site, interpretation of the archaeological record, palaeoenvironmental changes, and the aspect of human adaptation and living strategies.

[7][16] Lastly, during the first excavations burials were uncovered near the entrance of the cave, the remains being in a fetal position, and decorated with shells and ochre.

In 1993, Janette Deacon and Michael Brett proposed a display area for the cave to preserve its integrity and avoid erosion and degradation.

Currently, a walkway leading to the site’s display exists, showing an intact section profile from the original excavations and illustrations that tell the story of the cave.