Growth during early life stages is critical to fish population persistence. Few studies explore how river discharge and thermal regimes impact growth dynamics of young-of-the-year (YOY) fishes. We used otolith biochronologies and generalised additive mixed models to partition the effects of age, individual, river, temperature, discharge, and variance in discharge on daily growth rates of YOY fishes with an opportunistic life-history strategy: Galaxias vulgaris and Gobiomorphus breviceps. Growth of both species increased with temperature. Galaxias growth decreased with discharge, while Gobiomorphus growth increased with lowered discharge but only to a point (ca. 1/3 of median discharge), after which growth plateaued. Floods had a strong negative effect on YOY growth. Our study systems and species had different characteristics to those that formed the basis of the Riverscape Recruitment Synthesis Model (RRSM) and may explain why our results were only partially consistent with flow predictions for opportunistic species of the RRSM. Further, Galaxias growth was a negative function of high-frequency, daily variation in flow, and we present testable hypotheses to explain this result.