The commitment to advance the protection of the North American Great Lakes and the Baltic Sea continues during the COVID-19 pandemic. The resilience of the research community was displayed as policy decisions were made for the first virtual conferences this year to share scientific findings and expertise in both regions. As this pandemic continues to challenge the world, countries have responded to the threat and continue to deal with the uncertainties of this wicked transboundary problem in many different ways. This article discusses key governance and policy issues that have been revealed thus far that can inform the governance of the transboundary North American Great Lakes and the Baltic Sea. Key lessons from the pandemic include waiting for total scientific certainty to act can lead to fatal consequences and our symbiotic connection with nature. Further insights from the pandemic include the importance of context, science-based leadership, institutional accountability, and acknowledging that nature knows no borders.