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1. Assuming that recruitment variation is one of the main sources of fish population and assemblage changes, it is necessary to understand how natural variations in the environment influence 0+ fish abundance. Temperature regimes play an important role in enhancing both spawning activity and survival during early larval fish development. Flow regime variation, which is a powerful source of stream disturbance, is another factor to be taken into account. 2. Responses to these variables need to be assessed using long-term datasets, since standard statistical approaches fail to provide a causal structure or to quantify the different effects. We therefore used a 26-year dataset to evaluate the respective effects of seven derived independent variables describing the effects of temperature and flow regimes on the 0+ juvenile abundance of eight fish species in the River Rhone. 3. A clustering procedure using the Kendall tau rank correlation coefficient was implemented and identified three groups of fish according to their synchronic variations in juvenile abundance; i.e. varying with decreasing juvenile abundance, slightly increasing juvenile abundance and increasing juvenile abundance. These clusters provided the basis for building hierarchical log-Poisson generalized linear models. The Bayesian paradigm gives a reliable framework for model selection, and the best model was determined using the Bayes Factor. 4. The posterior distribution of the regression parameters was coherent with what was expected based on knowledge of the biology of the different species. It indicates that temperature regime drives 0+ juvenile abundance but that flow regime also plays an important regulating role. The models thus detected evidence of the consequences of specific flow events such as larval drift and an increase in available habitat during higher flow discharges. 5. Our study illustrates the advantages of using a hierarchical modelling approach to quantify ecological effects by improving discrimination between the different sources of uncertainty, leading to better precision when estimating regression parameters.