The transport of sand in saltation is driven by the persistently unsteady stresses exerted by turbulent winds. Based on coupled high-frequency observations of wind velocity and sand flux on a desert dune during intermittent saltation, we show here how observations of saltation by natural winds depend significantly on the timescale and method used for determining shear stress and sand flux. The correlation between sand flux and excess shear stress (stress above a threshold value) systematically improves for longer averaging timescale, T, and is better for stress determined by the law-of-the-wall versus the Reynolds stress method. Fitting parameters for the stress-flux relationship do not converge with increasing T, which may be explained by the nonstationary nature of wind velocity statistics. We show how it may be possible, based on the scale-dependent statistics of stress fluctuations, to rescale saltation flux predictions for wind observations made at different timescales. However, our observations indicate hysteresis and time lags in thresholds for initiation and cessation of saltation, which complicate threshold-based approaches to predicting sediment transport at different timescales.