Amblypygids use a pair of modified walking legs (antenniform) as chemosensory and mechanosensory appendages. At the tip of these legs are covered in chemosensory sensilla, which the animals use to sample odor stimuli in their environment by moving the antenniform leg through the air. We designed a set of experiments to measure the filtering effect that aerodynamic boundary layers have on the temporal and spatial structure of chemical stimuli. In addition, two different species of amblypygids (Paraphrynus laevifrons and Phrynus marginemaculatus) that live in two distinct habitats were used for a comparative analysis. Pulses of a tracer molecule were quantified at different distances and flow velocities using an electrochemical detection system. Temporal attributes of the chemical pulses were extracted and were statistically compared across velocities, distances from the appendage, and the two species. Overall, the boundary layer significantly decreased the concentration and increased the duration of pulses for both species. This filtering effect was more pronounced for P. marginemaculatus than P. laevifrons, as the chemical signal was lower in concentration and longer in duration at any distance from the antenniform leg. It is speculated that the difference in boundary layer filtering, as a function of appendage morphology, is tuned to the different types of odor plumes in these animals’ native habitats.