In this study, the benefits of accounting for nonzero vertical (interchannel) correlation for both the Advanced Technology Microwave Satellite (ATMS) and Infrared Atmospheric Sounding Interferometer (IASI) in the NRL Atmospheric Variational Data Assimilation System-Accelerated Representer (NAVDAS-AR) are assessed. The vertical observation error covariance matrix for the ATMS and IASI instruments was estimated using the Desroziers method (Desroziers et al., 2005). The results suggest lowering the assigned error variance and introducing strong correlations, especially in the moisture-sensitive channels. Strong positive impact on forecast skill (verified against both European Centre for Medium-Range Weather Forecasts (ECMWF) analyses and high quality radiosonde data) is shown in both the ATMS and IASI instruments. Additionally, the convergence of the iterative solver in NAVDAS-AR can be improved by small modifications to the observation error covariance matrices, resulting in further reduction in RMS error.