An artificial floods program has been implemented on the Sarine residual flow reach, downstream of the Rossens dam. Two artificial floods were released in 2016 (coupled with sediment augmentation) and in 2020. A natural flood occurred in 2021. The indicator set on habitat diversity (FOEN) was applied on a Sediment Augmentation and a Control Reach after each flood. Additional data sets comprise the macrohabitats, trout redds and population evolution. The effects of the 2020 artificial flood and the 2021 natural flood on the hydromorphology, the trout reproduction sites and population were compared. To generalize the previous results, hydrological descriptors were analyzed for statistical correlation with the hydromorphological and ecological responses of the river. Results show that the natural flood was larger and had a significantly higher morphological impact, reflected in the increase of the trout redds surface area. The decline in hydromorphological diversity underlines the lack of sediment supply. The correlation analysis confirms the importance of gravel bars as an indicator for trout redds. The role of morphogenic floods for redds availability and hence for trout population is also emphasized. The Sarine residual flow reach’s need for regular morphogenic floods, coupled with adequate sediment augmentation measures, is highlighted.