Artificial high flows attempt to simulate natural flood pulses in flow-regulated rivers with the intent to improve their ecological integrity. The long-term use of such high flow events have shown beneficial ecological effects on various rivers globally. However, such responses are often non-linear and characterized by underlying feedback mechanisms among ecosystem components. The question arises as to what happens when such high flow releases are disrupted or even discontinued. Here, we used the long-term (22 years) monitoring dataset from the river Spöl to examine whether discontinuation (2016–2021) of the flood program (annual artificial high flows from 2000 to 2016) resulted in the ecological degradation of the river. We used monitoring data of physico-chemistry, periphyton, benthic organic matter, macroinvertebrates and fish (brown trout, Salmo trutta fario L.) in the analysis. The flood program had no long-term effect on water physico-chemistry with most parameters showing typical variations associated with season and inter-annual weather patterns. The floods were effective at mobilizing bed sediments that reduced periphyton biomass and benthic organic matter following each flood. Increases in periphyton biomass and benthic organic matter occurred between floods, but both parameters showed no significant increase with discontinuation of the flood program. Floods reduced macroinvertebrate densities, but with density increases occurring between floods. The pulsed disturbances, and the progressive change in the habitat template, resulted in shifts in community assembly by reducing densities of Gammarus fossarum, a dominant crustacean, which allowed other taxa to colonize the system. Macroinvertebrate densities remained low after discontinuation of the floods, although G. fossarum densities have increased substantially while other taxa, especially some stoneflies, remained low in abundance. Notably, community assembly returned to a pre-flood composition with discontinuation of the floods. The abundance of brown trout increased substantially during the flood program but returned to low pre-flood numbers with discontinuation of the floods. We conclude that the flood program was beneficial to the ecology of the river Spöl and discontinuation of the floods resulted in degradation of the system after a relatively short lag period. However, the system showed high resilience to an earlier perturbation, a sediment spill in 2013, suggesting a rapid positive response by biota with resumption of the flood program.