While marine bryozoans were shown to be a promising source of bioactive compounds with the potential to be developed into drugs, their freshwater counterparts remain understudied. Considering that bioactive compounds isolated from bryozoans may originate from bacterial communities associated with the hosts, we explored the bacterial community of the freshwater bryozoan Cristatella mucedo using genomics and metabolomics. 16 S rRNA gene amplicon sequencing of the bacterial community associated with C. mucedo showed a considerable overlap with communities from surrounding water and sediment. Using different isolation approaches we retrieved a diverse collection of bacterial strains representing 26 genera, including a potentially new one. Genome sequencing and analyses of representative isolates of each genus revealed considerable potential for secondary metabolite biosynthesis. The secondary metabolomes of both mono- and co-cultures of selected isolates and enriched bryozoan-derived communities were investigated, allowing the identification of several known and potentially novel secondary metabolites. This work provides important information regarding the composition of the bacterial community associated with C. mucedo and sets the stage for its further exploration and exploitation for drug discovery.