Lake Mälaren is a complex lake, that provides ecosystem services to Sweden’s most populous region. These include access to bathing water, fishing grounds, and the raw water input that provides drinking water to over two million people. Major changes in water quality that affect the color of water, organic matter content or temperature may potentially have a large negative impact on the lake and the provisioning of ecosystem services. By working on Mälaren our results will be relevant to a large portion of Sweden’s population, and in the process of carrying out this project we will develop an openly available modeling system for Lake Mälaren. Presently there is no such modeling system that can be used to evaluate ongoing and short- and long-term changes to the entire lake that includes biogeochemical processes. This project will therefore be a significant contribution towards a better understanding and planning of the lake’s ecosystem services that will have importance for Sweden’s economy.