This study explores the effect of rearing environment on water bacterial communities (BC) and the association with those present in the gut of Nile tilapia larvae (Oreochromis niloticus, Linnaeus) grown in either recirculating or active suspension systems. 454 pyrosequencing of PCR-amplified 16S rRNA gene fragments was applied to characterize the composition of water, feed and gut bacteria communities. Observed changes in water BC over time and differences in water BCs between systems were highly correlated with corresponding water physico-chemical properties. Differences in gut bacterial communities during larval development were correlated with differences in water communities between systems. The correlation of feed BC with those in the gut was minor compared to that between gut and water, reflected by the fact that 4 to 43 times more OTUs were shared between water and gut than between gut and feed BC. Shared OTUs between water and gut suggest a successful transfer of microorganisms from water into the gut, and give insight about the niche and ecological adaptability of water microorganisms inside the gut. These findings suggest that steering of gut microbial communities could be possible through water microbial management derived by the design and functionality of the rearing system.