<p>Headwater non-floodplain wetlands are often overlooked in nutrient-management strategies despite their potential to regulate downstream water quality. Here we test whether headwater non-floodplain wetlands act as nutrient gatekeepers in the Lake Winnipeg Watershed. We define wetlands as seasonally-to-persistently inundated surface-water areas mapped from satellite imagery, and combine multi-decadal observations of wetland inundation and wetland–stream connectivity (1984–2020) with observed annual total nitrogen and total phosphorus loads (1994–2020) and random forest models. Nutrient export is lowest when headwater non-floodplain wetlands remain hydrologically disconnected and increases during episodic reconnection, indicating a threshold-like shift from nutrient storage to export. The ratio of disconnected non-floodplain wetland area is the strongest negative predictor of nutrient delivery, whereas mid/high-order reaches are weaker and less consistent. These results identify intermittently connected headwater non-floodplain wetlands as basin-scale regulators of nutrient pathways and highlight protecting them as a scalable strategy to reduce eutrophication risk in climate-sensitive watersheds.</p>