Gypsum saturation index
A geochemical model, like phreeqc calculates the saturation index (SI) for minerals based on the composition of the solution, temperature, and possibly pressure. These are used to calculate the activities of the ions, based on the activity coefficients. These are then compared to the activities that would be present at saturation as defined by the solubility product (Ksp). The saturation index is &lt; 0 if the solution is undersaturated with respect the mineral, = 0 at saturation, and > 0 if supersaturated.

So when you say the model shows you are saturated with respect to gypsum, it indicates that by definition you are in equilibrium with solid phase gypsum. It does not indicate if you got there by dissolving gypsum or by precipitating gypsum. It is highly unlikely (but theoretically possible) that your SI is exactly 0 without one of those things happening.