Governments worldwide do not adequately protect their limited freshwater systems and therefore place freshwater functions and attendant ecosystem services at risk. The best available scientific evidence compels enhanced protections for freshwater systems, especially for impermanent streams and wetlands outside of floodplains that are particularly vulnerable to alteration or destruction. New approaches to freshwater sustainability — implemented through scientifically informed adaptive management — are required to protect freshwater systems through periods of changing societal needs. One such approach introduced in the US in 2015 is the Clean Water Rule, which clarified the jurisdictional scope for federally protected waters. However, within hours of its implementation litigants convinced the US Court of Appeals for the Sixth Circuit to stay the rule, and the subsequently elected administration has now placed it under review for potential revision or rescission. Regardless of its outcome at the federal level, policy and management discussions initiated by the propagation of this rare rulemaking event have potential far-reaching implications at all levels of government across the US and worldwide. At this timely juncture, we provide a scientific rationale and three policy options for all levels of government to meaningfully enhance protection of these vulnerable waters. A fourth option, a 'do-nothing' approach, is wholly inconsistent with the well-established scientific evidence of the importance of these vulnerable waters.