Industrial and urban activities are major contributors to metal contamination in coastal systems, often impacting the physiology, distribution and diversity of marine invertebrates. This study assessed metal contaminations in sediments, seawater, algae and invertebrates across four armoured systems (harbours) and two natural sites along the south coast of South Africa. Bioaccumulation factors such as Biosediment (BSAF), Biowater (BWAF), Bioaccumulation (BAF) and bioremediation of metals by invertebrate bioindicators were also determined. Spatial variation in metal concentrations were observed, however, bioaccumulation of metals was site and species-specific. Invertebrates bioaccumulated higher metal concentrations in armoured than natural sites, with filter feeders exhibiting higher concentrations than grazers. Among filter feeders, Octomeris angulosa and Crassostrea gigas bioaccumulated elevated aluminium (Al), arsenic (As), chromium (Cr), zinc (Zn) and copper (Cu), while, Perna perna accumulated elevated nickel (Ni), cadmium (Cd) and lead (Pb). Among grazers, Siphonaria serrata and Scutellastra longicosta bioaccumulated elevated Al, Cr, Cd, cobalt (Co), Cu, Ni and Zn. Bioaccumulation factors indicated that (As, Ni, Zn) were bioaccumulated by algae, and invertebrates from sediment (BSAF>1) and from seawater (BWAF>1). Additionally, invertebrates bioaccumulated metals from their prey item, algae as indicated by (BAF>1). Arsenic Cd and Pb in invertebrates were above the maximum limit set for human consumption by various regulatory bodies. Our findings underscore the significant role of coastal invertebrates in bioaccumulating and bioremediating metals, suggesting a natural mechanism for water quality enhancement, especially in urbanised coastal areas.