Four sites following the salinity gradient of the Incomati River Estuary E1 (0-3NST), E2 (3-5NST), E3 (6-18NST) and E4 (19-27NST) were selected for the study. The aim of the study was to use free-living marine nematodes as pollution indicators in an area strongly affected by anthropogenic activities. Multivariate statistical analyses were used to determine the relationship between different environmental factors and with free-living marine nematodes. Metals such Cadmium, Colbat, Chromium, Copper, Iron, Manganese, Nickel, Vadium, Zinc and Aluminium influenced the diversity and density of free-living nematodes. Shannon-Wiener Diversity, Maturity Index and colonize-persisters percentage (c% - p%) were found to be good tools for use as pollution indicators in the study. Nematode genera such as Terschellingia, Theristus and Halalaimus were found to be dominant at a site strongly impacted by both metals concentration and organic matters. The three genera are believed to be good indicators of pollution in the Incomati River Estuary. It is recommended that further studies are done along the Mozambican Coast to identify nematodes that can be used as pollution indicators.