Since the mid-1970s, successful Lake Ontario management actions including nutrient load and pollution reductions, habitat restoration, and fish stocking have improved Lake Ontario. However, several new obstacles to maintenance and restoration have emerged. This special issue presents management-relevant research from multiple agency surveys in 2011 and 2012 and the 2013 Cooperative Science and Monitoring Initiative (CSMI), that span diverse lake habitats, species, and trophic levels. This research focused on themes of nutrient loading and fate; vertical dynamics of primary and secondary production; fish abundance and behavior; and food web structure. Together these papers identify the status of many of the key drivers of the Lake Ontario ecosystem and contribute to addressing lake-scale questions and management information needs in Lake Ontario and the other Great Lakes and connecting water bodies.