Natural organic matter (NOM, or humic substance) has a known tendency to form colloidal aggregates in aqueous environments, with the composition and concentration of cationic species in solution, pH, temperature, and the composition of the NOM itself playing important roles. Strong interaction of carboxylic groups of NOM with dissolved metal cations is thought to be the leading chemical interaction in NOM supramolecular aggregation. Computational molecular dynamics (MD) study of the interactions of Na+, Mg2+, and Ca2+ with the carboxylic groups of a model NOM fragment and acetate anions in aqueous solutions provides new quantitative insight into the structure, energetics, and dynamics of the interactions of carboxylic groups with metal cations, their association, and the effects of cations on the colloidal aggregation of NOM molecules. Potentials of mean force and the equilibrium constants describing overall ion association and the distribution of metal cations between contact ion pairs and solvent-separated ions pairs were computed from free MD simulations and restrained umbrella sampling calculations. The results provide insight into the local structural environments of metal-carboxylate association and the dynamics of exchange among these sites. All three cations prefer contact ion pair to solvent-separated ion pair coordination, and Na+ and Ca2+ show a strong preference for bidentate contact ion pair formation. The average residence time of a Ca2+ ion in a contact ion pair with the carboxylic groups is of the order of 0.5 ns, whereas the corresponding residence time of a Na+ ion is only between 0.02 and 0.05 ns. The average residence times of a Ca2+ ion in a bidentate coordinated contact ion pair vs a monodentate coordinated contact ion pair are about 0.5 and 0.08 ns, respectively. On the 10 ns time scale of our simulations, aggregation of the NOM molecules occurs in the presence of Ca2+ but not Na+ or Mg2+. These results agree with previous experimental observations and are explained by both Ca2+ ion bridging between NOM molecules and decreased repulsion between the NOM molecules due to the reduced net charge of the NOM-metal complexes. Simulations on a larger scale are needed to further explore the relative importance of the different aggregation mechanisms and the stability of NOM aggregates.