Water activity and related thermodynamic properties are calculated for several aqueous solutions using equilibrium molecular dynamics in conjunction with the recent extension of the Kirkwood-Buff (KB) theory for closed systems. The general applicability of this method is evaluated on aqueous mixtures of ethanol, glyoxal, malonic acid, and NaCl, which represent different types of condensed-phase interactions. Solution microstructures are analyzed using KB integrals and cluster analysis to identify molecular associations due to hydrophobic interactions, hydrate formation, hydrogen bonding, or electrostatic forces affecting solution nonideality in the different systems. Activity estimation by this implementation-subvolume-KB molecular dynamics, or SKBMD, simulation-agrees well with experimental measurements and UNIFAC calculations over a wide range of nonideality, with the exception of the malonic acid/water system. Systematic deviations for this system are attributed to the deficiency of the standard OPLS force field, and are partially remediated with a Non-Bonded FIX (NBFIX) correction to reduce its extensive hydrogen-bonded clustering. Comparison of water and solute excess chemical potentials against other molecular simulation techniques for NaCl/water mixtures shows the SKBMD method to be competitive in performance with those requiring additional external constraints or computational complexity. Equilibrium molecular dynamics and KB theory can therefore be suitable for estimation of solution properties and testing the suitability of force fields, though strongly associating components leading to large and long-lived molecular clusters (either in reality or as a result of a bias in atom-atom potentials) can lead to inefficient sampling and higher estimation errors.