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Large numbers of Finnish lakes accumulate biomass sediments due to large nutrient inputs from forest areas, agricultural and industrial activities. The theoretical biofuel production potential was studied for lake bottom biomass from mesotrophic (ML) and eutrophic lakes (EL) in eastern Finland. Methane potentials of the EL and ML biomass were 136.6 ml g−1 volatile solid and 38.9 ml g−1 volatile solid, respectively. The estimated ethanol yields of the EL and ML biomass from fermentation were 137 l tonne−1, and 40 l tonne−1, whereas the yields from mixed alcohol synthesis after gasification were 244.5 l tonne−1 and 57.1 l tonne−1, respectively. The ash from both lake bottom biomass contained harmful elements below the detectable limit, and therefore, could be used as fertilizer. Techno-economic estimation showed that bioethanol production from the fermentation of EL biomass is the most profitable process and is a potential non-food lignocellulosic biomass source for the biorefining industry.