Although soluble hydrocarbons persist for only hours to days in aquatic environments, they potentially pose a high toxicity to aquatic biota. Here we investigate effects of the water-soluble fraction (WSF) of crude oil on estuarine meiofauna, with special focus on nematodes. Copepods and amphipods were the most sensitive taxa, disappearing almost completely within 3 weeks after exposure. In nematodes, we observed mostly sublethal short-term effects of WSF, such as changes in feeding-type composition and age structure. In the longer term (months), total nematode density and species composition were significantly affected, whereas different diversity indices did not exhibit significant responses. Deposit-feeding and predatory nematodes were the most affected feeding types. Nevertheless, sensitivity was species-specific, with sometimes opposing responses between even congeneric species. Our results demonstrate the need to assess WSF effects on communities at the species level and over time periods well exceeding the residence time of the WSF in the environment.