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This article extends a recently proposed heterogeneous data assimilation technique for site characterization to estimate compression and shear wave velocity (Vp and Vs, respectively) and damping at Treasure Island and Delaney Park downhole arrays. The adopted method is based on the joint inversion of earthquake acceleration time series and experimental surface wave dispersion data, and including physical constraints to improve the inverse problem's well-posedness. We first use synthetic data at these two sites to refine the proposed approach and then apply the refined algorithm to real data sets available at the Treasure Island and Delaney Park downhole arrays. The joint inversion results show that the estimated Vs and Vp profiles are in very good agreement with measured profiles at these two sites. Our synthetic and real data experiment results suggest that Vp estimation from inversion at downhole arrays can be improved by integrating the water table depth information or the higher modes of the Rayleigh wave dispersion data. Depending on the site complexity, water table information can also help reduce uncertainties associated with damping estimation. In the last part of this article, we compare the performance of the inverted profiles to other methods used to incorporate spatial variability and wave scattering effects in 1D ground response analysis (GRA). The comparisons show that the joint inversion-based Vs and Vp profiles and damping ratios estimated in this article can effectively integrate the effects of spatial variability and wave scattering into 1D GRAs, especially at the Delaney Park downhole array, which is classified as a poorly modeled site using traditional 1D GRA.