A high-quality estimate of wind fields can potentially improve the safety and performance of Unmanned Aerial Vehicles (UAVs) operating in dense urban areas. Computational Fluid Dynamics (CFD) simulations can help provide a wind field estimate, but their accuracy depends on the knowledge of the distribution of the inlet boundary conditions. This paper provides a real-time methodology using a Particle Filter (PF) that utilizes wind measurements from a UAV to solve the inverse problem of predicting the inlet conditions as the UAV traverses the flow field. A Gaussian Process Regression (GPR) approach is used as a surrogate function to maintain the real-time nature of the proposed methodology. Real-world experiments with a UAV at an urban test-site prove the efficacy of the proposed method. The flight test shows that the 95% confidence interval for the difference between the mean estimated inlet conditions and mean ground truth measurements closely bound zero, with the difference in mean angles being between -3.680 degrees and 1.250 degrees and the difference in mean magnitudes being between -0:206 m/s and 0:020 m/s.