The lakes component of the Transboundary Waters Assessment Program (TWAP) was undertaken to compare the relative threats to transboundary lakes (and implicitly all “lentic waters”). Because of the greater complexity characterizing transboundary lake basins and their ecosystem services, compared to other freshwater systems, adopted management approaches must lead to a well-coordinated global process to address such challenges if their sustainability is to be attained. The assessment methodology must not only identify transboundary lake basin threats, but also help all involved basin stakeholders fully understand the need for collaborative efforts directed to gradual, incremental and long-term lake basin governance improvement.