Several pre-emergent herbicides (azafenidin, oxyfluorfen, and imazaquin–pendimethalin mixture), used for weed control during the establishment of short-rotation willow plantings, were tested for their impact on population density, species richness, and community structure of predaceous (Gamasina) and saprophagous and (or) mycophagous (Oribatida) soil mites. The experimental control was hand-weeded (no herbicide). Two site preparation treatments were used: conventional (disked) and erosion controlled (no-till with cover crop of winter rye). The influence of herbicide application on non-target organisms (soil mites) cannot be generalized, with groups being differentially affected. Overall, Oribatida were most affected by herbicides. Among specific herbicides, azafenidin and oxyfluorfen had a negative effect on density and species richness of soil mites. The response of Oribatida and Gamasina to herbicides was species-specific. Two species of Oribatida ( Sellnickochthonius immaculatus (Forsslund) and Liochthonius lapponicus (Trägårdh)) declined significantly in all herbicide-treated plots. The cover crop residue had positive effect on both Oribatida and Gamasina; the negative effect of herbicides on Oribatida was greatly mitigated by cover crop. Herbicides appear to reduce mite diversity and alter community structure, but they do not always affect abundance. We speculate that the sensitivity of Oribatida to herbicides can reflect the indirect impacts of herbicides on soil microflora.