Free-living nematodes were investigated in the Mar Piccolo of Taranto (Ionian Sea), a semi-enclosed basin of strategic importance for its complex productive infrastructure but in need of remediation due to the alarming amounts of heavy metals and synthetic organic contaminants in the sediments. Abundance, genera composition, biodiversity and trophic traits of nematodes were related to the gradual transition from marine to more brackish conditions and to the varying levels of contaminants in different sub-areas of the basin. Nematodes were more abundant and diverse at the most marine site while low numbers and diversity characterized the most contaminated station. Going towards the innermost part of the basin, gradually increasing values of abundance and biodiversity were observed although the assemblage was susceptible to the organic enrichment caused by mussel farms. The use of nematodes as ecological indicators mirrored the response of the assemblage to the main patterns acting in the basin (High/Good scores at the most marine site and Poor/Bad scores at the most contaminated station), giving a clear indication of environmental quality to stakeholders/authority that can contribute to address remediation actions in contaminated sediments.