Biomineralization creates complex structures with advantageous properties, such as the superior toughness seen in nacre. In biomineral nucleation, calcium carbonate or calcium phosphate ions are directed by organic macromolecules, often leading to the growth of thermodynamically unfavorable polymorphs and/or specifically shaped crystals that contribute to the materials’ properties. To investigate how macromolecules guide crystal formation in complex biological systems, we probed the pre-nucleation nanoscale interactions in a simplified computational model that may govern overall precipitation and crystallization. We performed atomistic molecular dynamics simulations of calcium carbonate solution with charged polymers as analogs to the proteins that have been shown to influence crystallization. By analyzing resulting polymer and ion configurations in this system, we found that ion aggregate size scales with concentration and is increased by the polymer’s presence. This effect is also shown to be impacted by polymer charge.