The site sits within the Greater Cape Floristic region, characterized by the fynbos biome; however the Klasies River Cave environment is mixed woods and shrubby brushland and maintains a temperate climate.

[5][4] While sea levels fluctuated over time, during certain occupations, the proximity to the coast and the surrounding grasslands provided marine life and terrestrial animals that were exploited by the caves inhabitants.

[6] From 1967–1968 John Wymer and Ronald Singer conducted excavations that revealed evidence of Middle Stone Age (MSA)-associated human habitation beginning approximately 125,000 years ago.

[4] Critiques of the original excavation include sampling bias due to excavation and screening methods, and combination of stratigraphic layers that obscures the sites' complexity; certain strata were lumped together making it difficult to differentiate between activities at the site and combining artifacts and bones from multiple different strata.

[1] Researchers have used microstratigraphic techniques to analyze and interpret the complex timeline of sediment deposition and post-depositional activities within the caves.

Because the cave system has so many varied layers and the different caves have different depositional characteristics and sediment properties, it has been hard to create a uniform system to group and chronologically group the layers for a site-wide comparison; natural processes such as erosion, and the influence of people at certain areas of the site (anthropogenic deposition of shell middens, hearths, etc.)

Paleoenvironment reconstruction uses multiple analytical foci to help determine a proximate estimate of the climate of a site during a given time frame.

[6] There is also evidence of forest-dwelling bovid and other animals that prefer wetland grasses and reeds (African marsh rat and hippopotamus), indicating the environmental diversity of the site during MSA II.

[2] Warm-water shellfish (brown mussels and other rocky shore species) and cape fur seals were present at the cave as groups were able to exploit marine food sources as well.

[citation needed] MSA III is marked by a declining temperatures and receding coastline that would have exposed the Palaeo-Agulhas Plain.

The study also noted that the use of certain plant types for survival during climate changes, and proposed that humans in the past could have subsisted in similar ways.

Howiesons Poort interrupts the relative uniformity seen in MSA I and MSA II: in the latter, large and long quartzite points and blades were the goal end products and were usually not retouched,[3] while the Howiesons Poort lithics were made from a wider variety of materials and were fashioned into smaller blades and artifacts.

[7] Bone tools have been found at KRM during the original excavations by Singer and Wymer coming from MSA II and Howiesons Poort strata.

[15] Three denticulated bone tools[15] originating from an MSA II context resemble musical rasps found at other Middle Stone Age sites in Southern Africa.

[16] Instead, the authors found starchy reside within the teeth of the rasp and suggest that the tool was used for plant processing rather than as an instrument or skin abrader, however this is not proven.

[11] The hominins at KRM were hunter-gatherers, and the presence of faunal remains, shellfish, and plant residues shows the wide variety of food sources available near the site.

Food consumption at the site consisted of marine and terrestrial animals, evidenced by shell middens and faunal remains of bovids.

[1][5] Scientists suggest that the wide availability and variation in food sources were the cause for the anatomically modern humans due to the nutrients required for larger brains and cognitive function.

[21] Plants within a 12.5 kilometer foraging radius of the caves would have included 161 native species from a mix of geophytes / underground storage organs (USOs), leaves, and fruits, all of which would provide sufficient nutrients for the hominins at the site.

[1] Cooked foods provide quickly digestible energy and would have contributed to a higher quality diet which could lead to an evolutionary change in Homo sapiens.

[5] Samples taken from hearths within MSA I and Howiesons Poort levels identified parenchyma, heated bones and shellfish found together indicating the cooking of multiple food sources.

[1][17] Two individuals appear to be deposited around the same time in one stratigraphic layer, but correlating a site-wide cannibalism event requires a finer-scale understanding of the lithostratigraphy that is not possible at present.

[citation needed] Assessment of relatedness between species is based on ancestral or derived traits to create a phylogeny that assigns closely related specimens to the same or similar groups; this is usually visualized as branches on a phylogenetic tree.

[23] Modern humans (Homo sapiens) originated in Africa and trace a lineage back to non-human primate ancestors there.

[15] Each sequence displays a different social convention for construction of stone tools (a techno-complex) that isn't based on raw material availability.

[15] Conventionalized artifact manufacture that is passed through generations is argued as symbolic behavior by Sarah Wurz, the current primary investigator at the site.

[15] KRM's bone tools represent this symbolic behavior as they exhibit similar modifications and use-wear patterns that suggest they were used and created in the same way.

At KRM higher concentrations of red ochre are found in the MSA I and Howiesons Poort levels which may be evidence of ritual or symbolic use.

However, taphonomic processes produce a bias towards sites where there is good preservation, skewing results and potentially obscuring the origin of behavioral modernity.

Arguments that state brain size, social demographics and other factors are the cause of behavioral modernity are undermined by these outside variables.