In this study, we investigate the impacts of two water treatment regimes, the closed aquaculture system (CAS) and flow-through system (FTS), on the carpet shell clam (Ruditapes decussatus) larval microbiota, growth and survival. A bacteriological barrier (B) was created among breeder stage treated by florfenicol (FF, 8 mg L -1 day -1 per 5 days). After spawning, larvae were maintained in five different rearing techniques: CAS; FTS; B ? CAS; B ? FTS and B ? CAS ? FF (8 mg L -1 day -1 per 3 days). Significant decrease was observed in both total bacterial count and presumptive Vibrio count (PVC) in FF-treated breeders. Besides, larvae reared in B ? FTS showed significantly lower PVC than larvae maintained in other rearing techniques. It was also determined that growth and survival of larvae reared in B ? CAS ? FF and B ? FTS were significantly better than those reared in other systems. One hundred and twelve Vibrio strains, isolated from breeders, eggs and larvae, were subjected to some bacteriological tests (API 20E strips, vibriostatic agent O/129, growth at different temperatures and salinity). Vibrio alginolyticus was the predominant isolated species (36.61 %), followed by V. fluvialis (25 %), V. vunificus (17.86 %), V. cholera (13.39 %) and V. paraheamolyticus (7.14 %). These results may contribute to the understanding of the effect of rearing techniques on the bacterial load, survival and growth of early life stages of R. decussatus larvae.