To date, passive flux meters have predominantly been applied in temperate environments for tracking the movement of contaminants in groundwater. This study applies these instruments to reduce uncertainty in (typically instantaneous) flux measurements made in a low‐gradient, wetland dominated, discontinuous permafrost environment. This method supports improved estimation of unsaturated and over‐winter subsurface flows which are very difficult to quantify using hydraulic gradient‐based approaches. Improved subsurface flow estimates can play a key role in understanding the water budget of this landscape.