Many microorganisms, including nematodes, ciliates, rotifers, cheatogastriches, and ostracods, have been found to be associated with freshwater snails in their natural habitats; some of these act as snail biocontrol agents. The current study sought to identify the microfauna associated with aquatic snails and how they interact to know if they have a role of snail biological control. During the 2020-2023 seasons, a survey of freshwater snails and their associated microfauna was conducted in the governorates of Giza and Qualyobyia in Egypt. The 18S ribosomal (18S rRNA) gene sequences for the new ciliate species were determined. The survey identified two snail parasitic nematodes, nine inquiline rotifers, nine ciliates (one of which, Euplotes elhusseini n.sp., was described morphologically and phylogenetically), one actinophryd, two gastrotrichs, and one ostracod was associated with five snail species from each of the Prosobranchiate and Pulmonate snails. The interaction between some microorganisms may affect their roles as control bioagents. Morphological and molecular characteristics of the new species, Euplotes elhusseini, were described. In conclusion, rotifers and snail parasitic nematodes are the only species that might be called control bioagents of harmful gastropods.