The objective of this study was to test the hypotheses that (1) free-living marine nematodes respond in a differential way to diesel fuel if it is combined with three trace metals (chromium, copper, and nickel) used as smoke suppressants and that (2) the magnitude of toxicity of diesel fuel differs according to the level of trace metal mixture added. Nematodes from Sidi Salem beach (Tunisia) were subjected separately for 30 days to three doses of diesel fuel and three others of a trace metals mixture. Simultaneously, low-dose diesel was combined with three amounts of a trace metal mixture. Results from univariate and multivariate methods of data evaluation generally support our initial hypothesis that nematode assemblages exhibit various characteristic changes when exposed to different types of disturbances; the low dose of diesel fuel, discernibly non-toxic alone, became toxic when trace metals were added. For all types of treatments, biological disturbance caused severe specific changes in assemblage structure. For diesel fuel-treated microcosms, Marylynnia bellula and Chromaspirinia pontica were the best positive indicative species; their remarkable presence in given ecosystem may predict unsafe seafood. The powerful toxicity of the combination between diesel fuel and trace metals was expressed with only negative bioindicators, namely Trichotheristus mirabilis, Pomponema multipapillatum, Ditlevsenella murmanica, Desmodora longiseta, and Bathylaimus capacosus. Assemblages with high abundances of these species should be an index of healthy seafood. When nematodes were exposed to only trace metals, their response looks special with a distinction of a different list of indicative species; the high presence of seven species (T. mirabilis, P. multipapillatum, Leptonemella aphanothecae, D. murmanica, Viscosia cobbi, Gammanema conicauda, and Viscosia glabra) could indicate a good quality of seafood and that of another species (Oncholaimellus mediterraneus) appeared an index of the opposite situation.