Eukaryotes may influence pollutant degradation processes in groundwater ecosystems by activities such as predation on bacteria and recycling of nutrients. Culture-independent community profiling and phylogenetic analysis of 18S rRNA gene fragments, as well as culturing, were employed to obtain insight into the sedimentassociated eukaryotic community composition in an anaerobic sandy aquifer polluted with landfill leachate (Banisveld, The Netherlands). The microeukaryotic community at a depth of 1 to 5 m below the surface along a transect downgradient (21 to 68 m) from the landfill and at a clean reference location was diverse. Fungal sequences dominated most clone libraries. The fungal diversity was high, and most sequences were sequences of yeasts of the Basidiomycota. Sequences of green algae (Chlorophyta) were detected in parts of the aquifer close (<30 m) to the landfill. The bacterium-predating nanoflagellate Heteromita globosa (Cercozoa) was retrieved in enrichments, and its sequences dominated the clone library derived from the polluted aquifer at a depth of 5 m at a location 21 m downgradient from the landfill. The number of culturable eukaryotes ranged from 10 2 to 10 3 cells/g sediment. Culture-independent quantification revealed slightly higher numbers. Groundwater mesofauna was not detected. We concluded that the food chain in this polluted aquifer is short and consists of prokaryotes and fungi as decomposers of organic matter and protists as primary consumers of the prokaryotes.Food webs in aquifers may comprise eukaryotes in addition to bacteria and archaea. Groundwater eukaryotes range from singlecelled heterotrophic nanoflagellates and fungi to amphipod crustaceans, each of which has important roles in the functioning of the groundwater ecosystem (8). The occurrence of fungi in low numbers has been described for a few pristine and polluted aquifers, but to our knowledge the identities and activities of these organisms have hardly been investigated (26,27,42). Protozoans, especially nanoflagellates, selectively graze on the biomass of the bacterial community (35) and recycle nutrients (36).The abundance of protists, such as ciliates and flagellates, generally increases when there is pollution (27, 35). Biodegradation of organic pollutants often results in the development of anaerobic conditions. Under anoxic conditions, protists can survive and affect the abundance and diversity of bacteria (20). Protists can indirectly affect contaminant biodegradation. By feeding on bacteria, protists can reduce degrader populations, negatively influencing the process of biodegradation (21, 49). However, protists can also positively contribute to organic contaminant degradation by recycling limiting nutrients and making them available to pollutant-degrading bacteria (36), stimulating the activity of each bacterium (29, 30), or sustaining bioremediation by maintaining hydraulic conductivity of the aquifer as a result of reduced bacterial clogging (31, 43).Landfill leachate is an important source of groundwater po...