The Åland Islands are feeding grounds for river- and sea-spawning whitefish (Coregonus lavaretus), including also hatchery-reared released whitefish. Management of fisheries requires knowledge of whitefish origin from their catches, but such information is deficient at the Åland Islands. The numbers of gill rakers had unique (discretized) Gaussian frequency distributions in all three forms studied. This justified the usage of Gaussian finite mixture models on gill raker data for estimating the proportions of the forms in mixed catches during the non-spawning season. From 14 catches at the Åland Islands from 2012–2013, on average 54.8% were river-spawning whitefish, while the presence of hatchery-reared, sea-spawning whitefish was low but uncertain. Using a hierarchical variant of the model, we showed that the proportion of river-spawning whitefish decreased from 69.6% in June to 38.3% in August. Our study provides feasible methods for monitoring spatio-temporal variation in the proportions of river- and sea-spawning whitefish.