Floating hapas (fine mesh net enclosures) are a cost‐effective ocean nursery system to culture post‐metamorphic Holothuria scabra to release size. The growth of periphyton biofilm on hapas is a natural food source for early juveniles. This study investigated the effects of periphyton quality (i.e. chlorophyll‐a, phaeopigment, total biomass, autotrophic index or AI), water quality (nutrients, chlorophyll‐a) and environmental parameters (temperature, rainfall) on the temporal variation in the growth and survival of early juvenile (~3 mm) H. scabra reared in floating hapas. Five trials where the juveniles were reared for 60 days each in the eutrophic coastal waters of Bolinao, the Philippines were conducted during different months over 2 years. Significant differences in the growth and survival of juveniles among trials were found. Absolute growth rates (AGR) ranged widely (0.01–0.09 g/day). Trials with high AGR of juveniles (0.07–0.09 g/day) during the first 30 days of rearing had significantly higher chlorophyll‐a (chl‐a) in biofilm (15.9–27.5 mg/m2) and lower AI. Conversely, during the subsequent 30 days, trials with high AGR of juveniles (0.06–0.11 g/day) had significantly lower chl‐a and higher AI. Multivariate analyses showed that chl‐a in biofilm, AI and nutrients in the water column are good indicators of periphyton quality and juvenile growth rates in floating hapas. Further, this study validates the expansion of the feeding mode of juveniles from primarily grazing on microalgae, to feeding on detritus and heterotrophs as they grow. These results are important in optimizing ocean nursery systems.