The stability of functionalized nanoparticles generally results from both steric and electrostatic interactions. Viruses like bacteriophage MS2 have adopted similar strategies for stability against aggregation, including a net negative charge under natural water conditions and using polypeptides that form loops extending from the surface of the protein capsid for stabilization. In natural systems, dissolved organic matter can adsorb to and effectively functionalize nanoparticle surfaces, affecting the fate and transport of these nanoparticles. We used time-resolved dynamic light scattering to measure the aggregation kinetics of a model virus, bacteriophage MS2, across a range of solution chemistries to determine what factors might destabilize viruses in aquatic systems. In monovalent electrolytes (LiCl, NaCl, and KCl), aggregation of MS2 could not be induced within a reasonable kinetic time frame, and MS2 was stable even at salt concentrations greater than 1.0 M. Aggregation of MS2 could be induced in divalent electrolytes when we employed Ca2+. This trend was also observed in solutions containing 10 mg/L Suwannee River organic matter (SROM) reference material. Even at Ca2+ concentrations as high 200 mM, diffusion-controlled aggregation was never achieved, demonstrating an additional barrier to aggregation. These results were confirmed by small-angle X-ray scattering experiments, which indicate a transition from repulsive to attractive interactions between MS2 virus particles as monovalent salts are replaced by divalent salts.