Value of the Data •These are the first metavirome data on the freshwater sponges Baikalospongia bacillifera. •The data provides valuable information about the diversity and functional potential of dsDNA viral communities in the sponge holobionts. •This data is useful for comparing viral communities in different marine and freshwater sponges. •Raw sequence data can be used for various additional bioinformatics processing. •The data can be used for investigations of sponge diseases