Lake Toba is a unique natural asset of global significance located in the North Sumatra Province of Indonesia. The Lake has a rich cultural heritage and provides a wide range of environmental goods and services, making it one of Indonesia’s priority tourism destinations for development. Sustaining the long-term economic and environmental value of Lake Toba depends on addressing the deterioration of water quality. A collaborative process involving local stakeholders, national agencies/ministries/organizations and international experts has proposed a set of investments to help improve water quality in Lake Toba. These investments are based on an assessment of the lake and its basin, and acknowledge the need for improved information, institutional coordination, and an Integrated Lake Basin Management Platform. More specifically, it recommends improvements in water quality can only be achieved through enforcement of policy measures relating to the carrying capacity of Lake Toba for aquaculture production. A comprehensive and integrated water quality monitoring plan with a shared information management platform is required to assess the outcomes of any intervention and adapt to changing circumstances. Cooperative institutional mechanisms are needed to provide an interagency platform and the enabling environment for the integrated management of Lake Toba.