The majority of seafood is produced from farming, with most finfish coming from freshwater ponds. Across continents, aquaculture is growing fastest in Africa at 11.7 % annual growth, thus improving production for fish farmers while ensuring seafood safety for human consumption is needed. To understand the probiotic or prebiotic effects of fertilizing freshwater ponds with livestock manure, we grew tilapia and catfish together for four weeks under seven manure treatments including layer chicken, broiler chicken, guinea fowl, quail, pig, cow, and standard commercial feed only and evaluated the microbial communities of the manure, water column, tilapia and catfish feces using 16S and 18S rRNA marker genes along with whole genome sequencing. Catfish growth, but not tilapia, was positively associated with microbial activity (P=0.0006, R2=0.4887) and greatest in ponds fertilized with quail manure (ANOVA, P&lt 0.05). Tilapia growth was highest in the broiler manure but not significant while tilapia fecal microbial richness (but not catfish) was positively correlated with microbial activity (P=0.0309, R2=0.2458). Animal manure was unique and influenced the bacterial microbiome in pond water, tilapia gut, and catfish gut and eukaryotic microbiome in pond water and catfish guts (PERMANOVA, P = 0.001). On average, 18.5%, 18.6%, and 45.3% of manure bacteria sOTUs were present in the water column, catfish feces, and tilapia feces which comprised 3.7%, 12.8%, and 10.9% of the total microbial richness of the communities, respectively. Antibiotic resistance genes were highest in the manure and water samples followed by tilapia feces and then lowest in catfish feces (P&lt 0.0001). In this study we demonstrate how the bacterial and eukaryotic microbial composition of fish ponds are influenced by livestock specific manure inputs and that the gut microbiome of O. shiranus is more sensitive and responsive than C. gariepinus to these changes. Since only 13 % of the core manure bacteria could be detected in the core pond water and fish gut communities we conclude that animal manure used as fertilizer induces a primarily prebiotic effect on the pond ecosystem rather than a direct probiotic effect on fish. We identify how the tilapia gut microbiome is more influenced by environmental microbes while African catfish growth benefits more from manure fertilization.