Since the 1950s,the International Joint Commission (IJC) of Canada and the United States has issued water regulation and management plans for Lake Ontario and the St. Lawrence River. Changes in recreational, environmental, navigational and other uses of the water system have prompted the IJC to consider replacing the current water regulation plan in operation for more than 40 years. IJC’s goals for a replacement plan include sound scientific foundations, public participation, transparency in plan development and evaluation, and inclusion of environmental considerations. To help develop and select the new plan, the IJC supported a 5-year, $20 million Lake Ontario-St. Lawrence River Study (LOSLR Study). The LOSLR Study uses models to compile and integrate data gathered from a series of commissioned studies of wetlands, species at risk, recreational boating, fisheries, coastal erosion and flooding, commercial navigation, hydropower, industrial, municipal and domestic water intakes, public information and education, and hydrologic modeling. This report reviews a portion of the study that focused on wetlands and species at risk and three of the models that were used. The report finds that the overall breadth of the LOSLR study is impressive, and commends the scale and inclusiveness of the studies and models. In terms of informing decision making, however, the reviewed studies and models show deficiencies when evaluated against ten evaluation criteria, including treatment of uncertainty, quality control/quality assurance, thorough documentation, and empirical foundations. Among the report’s recommendations is a need for more thorough documentation of study methods and findings, stronger and more consistent quality control, and more attention to how uncertainty should be addressed to better inform decision making. This NRC study was conducted in collaboration with the Royal Society of Canada.