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Unmanned Aerial Vehicles (UAVs) are a popular platform for air quality measurements. For vertical measurements, rotary-wing UAVs are particularly well-suited. However, an important concern with rotary-wing UAVs is how the rotor-downwash affects measurement accuracy. Measurements from a recent field campaign showed notable discrepancies between data from ascent and descent, which suggested the UAV downwash may be the cause. To investigate and explain these observed discrepancies, we use high-fidelity computational fluid dynamics (CFD) simulations to simulate a UAV during vertical flight. We use a tracer to model a gaseous pollutant and evaluate the impact of the rotor-downwash on the concentration around the UAV. Our results indicate that, when measuring in a gradient, UAV-based measurements were ∼50% greater than the expected concentration during descent, but they were accurate during ascent, regardless of the location of the sensor. These results provide an explanation for errors encountered during vertical measurements and provide insight for accurate data collection methods in future studies.