Aeolian sediment traps are widely used to estimate the total volume of wind-driven sediment transport, but also to study the vertical mass distribution of a saltating sand cloud. The reliability of sediment flux estimations from such measurements are dependent upon the specific configuration of the measurement compartments and the analysis approach used. In this study, we analyse the uncertainty of these measurements by investigating the vertical cumulative distribution and relative sediment flux derived from both wind tunnel and field studies. Vertical flux data was examined using existing data in combination with a newly acquired dataset; comprising meteorological data and sediment fluxes from six different events, using three customized catchers at Ameland beaches in northern Netherlands. Fast-temporal data collected in a wind tunnel shows that the median transport height has a scattered pattern between impact and fluid threshold, that increases linearly with shear velocities above the fluid threshold. For finer sediment, a larger proportion was transported closer to the surface compared to coarser sediment fractions. It was also shown that errors originating from the distribution of sampling compartments, specifically the location of the lowest sediment trap relative to the surface, can be identified using the relative sediment flux. In the field, surface conditions such as surface moisture, surface crusts or frozen surfaces have a more pronounced but localized effect than shear velocity. Uncertainty in aeolian mass flux estimates can be reduced by placing multiple compartments in closer proximity to the surface.