Biominerals are crucial materials that play a vital role in many forms of life. Understanding the various steps through which ions in aqueous environment associate to form increasingly structured particles that eventually transform into the final crystalline or amorphous poly(a)morph in the presence of biologically active molecules is therefore of great significance. In this context, computer modeling is now able to provide an accurate atomistic picture of the dynamics and thermodynamics of possible association events in solution, as well as to make predictions as to particle stability and possible alternative nucleation pathways, as a complement to experiment. This review provides a general overview of the most significant computational methods and of their achievements in this field, with a focus on calcium carbonate as the most abundant biomineral.