Strategies to improve covariance estimates for ensemble-based assimilation of near-surface observations in atmospheric models are explored. It is known that localization of covariance estimates can improve conditioning of covariance matrices in the assimilation process by removing spurious elements and increasing the rank of the matrix. Vertical covariance localization is the focus of this work, and two basic approaches are compared: 1) a recently proposed hierarchical filter approach based on sampling theory and 2) a more commonly used fifth-order piecewise rational function. The hierarchical filter allows for dynamic estimates of localization functions and does not place any restrictions on their form. The rational function is optimized for every analysis time of day and for every possible observation and state variable combination. The methods are tested with a column model containing PBL and land surface parameterization schemes that are available in current mesoscale modeling systems. The results are expected to provide context for assimilation of near-surface observations in mesoscale models, which will benefit short-range mesoscale NWP applications. Results show that both the hierarchical and rational function approaches effectively improve covariance estimates from small ensembles. The hierarchical approach provides localization functions that are irregular and more closely related to PBL structure. Analysis of eigenvalue spectra show that both approaches improve the rank of the covariance matrices, but the amount of improvement is not always directly related to the assimilation performance. Results also show that specifying different localization functions for different observation and state variable combinations is more important than including time dependence.