Although epibiont ciliates make up a significant part of the biomass in aquatic ecosystems and may cause perceptible alterations in the population dynamics of their hosts, studies on the extrinsic and intrinsic factors that control the abundance of these microorganisms are scarce in literature. In the present study, we investigated the colonization site and intensity of rhabdostylid epibiont upon chironomid larvae and assessed the influence of organic pollution and chironomid communities on the prevalence and abundance of epibiont ciliates at five sampling stations (two in rural areas and three in urban areas) along a neotropical urban stream over a period of 12 months. Among the 24 genera of chironomids found and the 31,976 larvae analyzed, 96.12% belonged to the Chironomus genus, of which 16.95% (5212) were colonized by Rhabdostyla aff. chironomi. The infestation intensity varied from one to 67 individuals per host with an average intensity of 4.86 (± 33.45). Ciliates were only found colonizing the chironomids' ventral tubules. The high number of chironomid larvae, high host- and site-specificity, low infestation intensity, and absence of apparent structural damage to hosts evidence an intimate relationship between epibiont and basibiont as well as a possibly long coevolutionary history. Both prevalence and abundance of epibiont ciliates were correlated to the pollution rate of the studied stream. There was an alteration in the composition and structure of the chironomid community along the sampling stations. Numeric dominance of Chironomus-tolerant chironomids and its direct correlation to infestation prevalence and to ciliates abundance highlights the predilection of both peritrich ciliates and Chironomus larvae for organically-enriched environments.