The uThukela shelf is a large section of the KwaZulu-Natal (KZN) Bight, and being situated adjacent to the largest river on South Africa’s east coast and the fluvially-dominated uThukela Estuary, is an excellent example of a fluvially-dependent coastal ecosystem. Previous studies found that this shelf contains structurally and functionally unique macroinvertebrate communities that contributed to the promulgation of the uThukela Marine Protected Area (MPA), as part of the South African MPA network of 20 new or extended systems. This study expands on this evidence using recent samples collected prior to the protection of the uThukela shelf to provide a good baseline database for future monitoring within the MPA. The uThukela macrofauna distributions and the environmental parameters correlated with these patterns were investigated through replicated sediment grabs that were collected with corresponding abiotic parameters, along coast-perpendicular transects. Macrofauna were subsequently classified taxonomically and their functional attributes determined. One replicate collected on the innershelf was particularly noteworthy as the taxa composition was unique and unexpected for a mud depocenter as it was indicative of hard substrata, suggesting a nearby low-lying reef. This habitat anomaly should be further investigated as it may play an important role in biodiversity and ecosystem functioning within the uThukela benthic system that mostly consists of soft sediments. Overall, the uThukela shelf soft-sediment community represented a wide variety of taxa but in low abundance, and was dominated by burrowing polychaetes. These ubiquitous polychaetes exhibited diverse biological traits, and a finding of this study was that this group alone is a potential surrogate for future studies and monitoring of the entire uThukela shelf macroinvertebrate community. This community consisted of mostly facultative deposit feeders that shift to suspension-feeding and rely significantly on terrestrial particulate organic matter (POM) and mud deposited onto the shelf by the fluvially-dominated uThukela Estuary. The adaptive behaviour of these taxa allows intermittent shifts in food acquisition when conditions do not favour this optimal deposition (such as during reduced fluvial outflow), thereby enhancing ecosystem resilience to natural environmental fluxes. Natural fluctuations in the uThukela River flow results in reduced freshwater penetration onto the shelf during the dry (winter) season, and was observed during this study by the higher-than-expected salinity measurements further inshore and the resultant atypical salinity gradient across the uThukela shelf. Salinity, along with dissolved oxygen, were the measured near-bottom water parameters most correlated with macrobenthic distribution. Sediment composition also affected distribution patterns, forming fine-grained and medium-coarse-grained assemblages on the inner and mid-shelf, and a muddy assemblage on the outer-shelf. The muddy outer-shelf is mostly old deposits that suggests the uThukela has functioned as a fluvially-dominated system for a long time. Overall, sediments contained a large amount of crushed-shell and high Foraminifera abundances, contributing to habitat complexity and increasing diversity. Maintaining macrofauna diversity by preserving benthic habitats is vital in the functional success of marine ecosystems; particularly so in the uThukela system that is classified as strongly benthic-driven. This study provides baseline information contributing to future monitoring of whether the uThukela MPA achieves the aim of protecting rare benthic habitats associated with the connection of the coast to the deep sea and whether macrofauna diversity and associated ecological processes are maintained. In addition, it will support future studies within the MPA that emphasise the importance of the critical role of freshwater to the marine system and that ensure areas important for life-history strategies of vertebrates and invertebrates with high conservation status are conserved.