Ephemeral streams (the small headwater rivers that only flow in response to rain events) have a complicated management history in the US. Yet, we need an explicit assessment of their contributions to downstream hydrology and water quality. To answer this question, we used high-performance computing to build a model for over 22,000,000 rivers, streams, and lakes across the United States (US). This revealed unexpectedly high ephemeral contributions to flow in larger, downstream rivers. Because ephemeral streams are no longer protected under the US Clean Water Act, this work identified a pathway through which unprotected water may flow into larger, protected rivers to the potential detriment of US water quality.