ObjectiveAs part of a large‐scale hydroelectric project, the mean annual flow of the Rupert River (northern Quebec, Canada) was reduced by 52% at its mouth in 2009. To protect fish habitat, an ecological flow regime that was modulated according to the biological seasons was implemented downstream from the diversion point. An 8‐year monitoring program, including 2 years before partial diversion, was carried out to verify the effectiveness of this mitigation measure on the total annual abundance of anadromous Coregoninae (Cisco Coregonus artedi and Lake Whitefish C. clupeaformis) larvae, which was used as biological indicator of recruitment success. The monitoring also aimed to determine the effects of flow modification on the timing of the larval drift and the spatial distribution of larvae in a river cross section.MethodsEach year, sampling consisted of installing drift nets during the entire downstream larval migration in a river cross section of the lower Rupert River. Drift nets were systematically placed to ensure representative sampling of the river section.ResultPrior to flow reduction, the estimated total number of larvae varied between 1.8 and 8.6 million. Over the following 6 years, the estimated larval population has remained steady at 3–4 million. Otherwise, larval drift characteristics have not changed since the flow reduction, as (1) the duration of the larval drift is the same as before, about 1 month in May and early June, with a peak period of about 8 days; (2) rise in water temperature in spring is a determining factor in the timing of larval drift; and (3) the larvae drift mainly near the surface of the water.ConclusionThe monitoring results indicate that the ecological flow regime implemented in the Rupert River was adequate to maintain anadromous coregonine populations.