The article considers the effect of ultraviolet (UV) radiation and ultrasound (US) on the qualitative and quantitative indicators of the filtration elements periphyton in a recirculation aquaculture system (RAS) under different treatment regimens. It is assumed that the combined effect of UV and US will improve the efficiency of water purification in the RAS and also contribute to the elimination of pathogenic microorganisms. It was shown that the maximum diversity of periphyton organisms was observed in the absence of UV and US action. A total of 26 taxonomic units were found, with some of them categorized as unclassified (Unclassified_Rotifer; Unclassified_Nematode). High relative frequency of occurrence was noted for the species Arcella vulgaris (16.86%), Centropyxis aculeata (21.03%), and Arcella sp. (16.86%) of the testate amoebae class in the control group. Ciliates were also represented by a large number of species. Of 10 infusoria 6 belonged to free-living forms and 4 to sessile forms. Vorticella convallaria (16.21%), Stylonychia pustulata (13.98%), Zoothamnium sp. (13.98%) had the highest relative occurrence in the control. Ultraviolet radiation led to changes in the abundance of certain groups of hydrobionts, in particular, representatives of ciliates and oligochaetes. Using a UV source reduced the relative frequency of Arcella sp. and Centropyxis sp. to 3.33 and 6.66% correspondingly, relative to the control. The combined impact of US and UV caused a significant decrease in the relative frequency of Ciliate and Oligoheata, but had little effect on testate amoebae and rotifers. According to the results obtained, it can be supposed that the presence of an additional source of US radiation contributes to the reduction of the number of free-living forms of parasitic infusoria and can prevent the development of microbial and parasitic diseases. Thus, additional studying the biofilter microbial community under the influence of UV and US radiation is required.