Eutrophication has been a major stressor in lakes during the last century, with important implications for fish populations and thus fisheries. We summarised the Arctic charr (Salvelinus alpinus) fishery data available in Lake Geneva between 1887 and 2011 to describe contemporary catches in a broad perspective in relationship to the trophic status and the stocking history. Actual catches are low, but such levels had already been reached before the period of eutrophication. In addition, the high catch levels during the 1990s appeared to be artificially boosted by intense stocking and therefore cannot be used as a reference point. Thus, fishery data only do not allow for population functionality inference. Subsequently, we evaluated the contemporary contribution of stocking to catches and to the spawners by marking all of the fingerlings stocked in 2007 (n = 993,300 individuals) with a mass marking otolith technique using alizarine Red S. Multiple markings allowed us to distinguish between three stocking practices and to compare their relative efficiency. From 2009 to 2011, 1929 charr were sampled in recreational catches, commercial catches, and in spawners. More than 51% (980) of the total sample set corresponded to the 2007 cohort. The total contribution of stocked fish was 84% at stage 2+, 72% at stage 3+, and 44% at stage 4+. The results were similar to prior values obtained during the 1980s. Differences in the contributions between the types of samples (commercial catches, recreational catches, and spawners) were found. The results highlighted the fact that the current stocking effectiveness was 4 to 5 times lower compared to the effectiveness during the 1980s. Consequently, the current concern about the Arctic charr population, and the fishery in Lake Geneva, is two-fold: first, the long process of reoligotrophication does not allow for the restoration of self-sustaining Arctic charr populations; second, the stocking effectiveness decreased strongly over the last 30 years. Even if stocking greatly contributes to catches, it still does not ensure a sustainable fishery at a high level.