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Bioindicators assess the mangroves ecological state according to the types of pressures but they differ with the ecosystem’s specificities. We investigated benthic meiofauna diversity and structure within the low human-impacted mangroves in French Guiana (South America) in response to sediment variables with various distances to the main city. Contaminant’s concentrations differed among the stations, but they remained below toxicity guidelines. Meiofauna structure (Foraminifera, Kinorhyncha, Nematoda) however varied accordingly. Nematode’s identification brought details on the sediment’s quality. The opportunistic genus <i>Paraethmolaimus</i> (Jensen, 1994) strongly correlated to the higher concentrations of Hg, Pb. Anoxic sediments were marked by organic enrichment in pesticides, PCB, and mangrove litter products and dominance of two tolerant genus, <i>Terschellingia</i> (de Man, 1888) and <i>Spirinia</i> (Gerlach, 1963). In each of these two stations, we found many <i>Desmodora</i> individuals (de Man, 1889) with the presence of epibionts highlighting the nematodes decreased fitness and defenses. Oxic sediments without contaminants were distinguished by the sensitive genera <i>Pseudocella</i> (Filipjev, 1927) and a higher diversity of trophic groups. Our results suggested a nematodes sensitivity to low contaminants concentrations. Further investigations at different spatio-temporal scales and levels of deterioration, would be necessary to use of this group as bioindicator of the mangroves’ ecological status.