A considerable number of lakes in Sweden have high phosphorus internal loading from the sediments which cause cyanobacterial blooms every summer. Due to potential risks with such blooms for human health, drinking water supply, and ecosystem services, measures need to be taken to control the phosphorus content. Measures to control the phosphorus input from the surrounding land has been in focus. However, the measures have not been sufficient. This is because phosphorus deposited at the bottom of the lakes for many years are finally starting to leak to the water phase when the decomposition of sediments leads to anoxic conditions. In order to determine effective and efficient lake restoration measures, methods for lake restoration decision support by a multi-criteria analysis and the application of a decision analysis are developed. The multi-criteria analysis includes the determination of costs, longevity, and efficacy of six common lake restoration measures to reduce internal phosphorous loads in two lakes selected as a case study. The results show that aluminum treatment combines a highest efficacy with a high-cost efficiency being thus the optimal identified measure. The method involves adding an aluminum solution to the lakes’ sediment, which binds phosphorus, preventing it to be released to the water column. The multi-criteria model is integrated to a decision analytical model. The decision analytical model is used to identify the monetary socio-economic and environmental boundaries for the implementation of the optimal lake restoration measure.