Although it is widely known that observations of aeolian sediment transport are susceptible to large sampling errors, sample designs are frequently used that do not sufficiently reduce the measurement uncertainties inherent in the study of aeolian processes. Here, we examine the influence of sample size (n) and sampling location on uncertainty in models of aeolian sediment transport responses to vegetation cover change. We compare measurements from a stratified random array of 27 horizontal sediment mass flux samplers to vegetative cover data collected at a 1 ha site over a period of nearly 6 years. To assess the sensitivity of modeled relationships between aeolian transport and vegetative cover to sample design, we analyze statistical regressions for all possible combinations of sample size and sampler locations. We show that at least 17 randomly located samplers are needed to consistently capture the sediment mass flux response to vegetative cover change. We found that multiple statistically significant models can describe the sediment flux-vegetative cover relationship when using smaller sample sizes, demonstrating the risks of inferring sediment transport response from an underpowered sample design. Across vegetative functional groups, we found that woody cover generally influenced aeolian sediment transport rates more than herbaceous cover, while model uncertainty at large sample sizes (n > 17) showed the limitation of using vegetative cover as an indicator of aeolian sediment transport. Our results suggest an evaluation of sampling practices in aeolian sediment transport studies may be needed to avoid inferential errors that are likely pervasive in this field of study.