Smaller body-sized invertebrate groups are known to be highly sensitive to environmental pollution. Like soil nematodes, enchytraeids have very permeable cuticles and come into direct contact with heavy metals; therefore they can be adversely affected by soil pollution. However, in contrast to nematodes, fewer data on enchytraeids are at our disposal to assess their functional responses to heavy metals. Such an assessment would be of greatest value, as in any edaphic community, enchytraeids are the only functional group bridging the detrital energy flux across the bacterial-driven and the fungal-driven pathways. For this purpose we investigated and evaluated the effect of heavy metals on the occurrence and biomass of enchytraeids in different soils in The Netherlands. Samplings of topsoils were carried out in 297 sites with Pleistocene sandy soils, river clay and sea clay under different environmental stress and all recovered enchytraeid species have been included in three existing phylogenetical clades (hereafter: A, B, and C). Our results show that the biomass of the enchytraeid species belonging to the Clade C is highly correlated with Cr, Cu and Zn in sandy soils (all 2-tails significance values share p < 0.005, n = 186) but is correlated with Cu and Hg in loamy soils (p < 0.05, n = 111), whilst the biomass of the enchytraeid species belonging to the Clade B is highly correlated with either Cd + Cu + Pb in sandy soils (p < 0.025, n = 186) or Hg + Pb in loamy soils (p < 0.05, n = 111). The entire enchytraeid community actively contributes to promote the rapid turnover of soil organic matter. Given that clay-rich soils retain a much higher amount of heavy metals in contrast to sandy soils, most enchytraeids share different values as bioindicators according to the soil type, even comparing river clay with sea clay. Hence, elemental availabilities have disproportionately strong effects on enchytraeids and on the entire edaphic community according to the soil types.