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The disparity in the impact of COVID-19 on minority populations in the United States has been well established in the available data on deaths, case counts, and adverse outcomes. However, critical metrics used by public health officials and epidemiologists, such as a time dependent viral reproductive number (\begin{document}$$ R_t $$\end{document}), can be hard to calculate from this data especially for individual populations. Furthermore, disparities in the availability of testing, record keeping infrastructure, or government funding in disadvantaged populations can produce incomplete data sets. In this work, we apply ensemble data assimilation techniques which optimally combine model and data to produce a more complete data set providing better estimates of the critical metrics used by public health officials and epidemiologists. We employ a multi-population SEIR (Susceptible, Exposed, Infected and Recovered) model with a time dependent reproductive number and age stratified contact rate matrix for each population. We assimilate the daily death data for populations separated by ethnic/racial groupings using a technique called Ensemble Smoothing with Multiple Data Assimilation (ESMDA) to estimate model parameters and produce an \begin{document}$$R_t(n)$$\end{document} for the \begin{document}$$n^{th}$$\end{document} population. We do this with three distinct approaches, (1) using the same contact matrices and prior \begin{document}$$R_t(n)$$\end{document} for each population, (2) assigning contact matrices with increased contact rates for working age and older adults to populations experiencing disparity and (3) as in (2) but with a time-continuous update to \begin{document}$$R_t(n)$$\end{document}. We make a study of 9 U.S. states and the District of Columbia providing a complete time series of the pandemic in each and, in some cases, identifying disparities not otherwise evident in the aggregate statistics.