Calcium carbonate (CaCO3) geochemical reactions exert a fundamental control on the evolution of porosity and permeability in shallow-to-deep subsurface siliciclastic and limestone rock reservoirs. As a result, these carbonate water–rock interactions play a critically important role in research on groundwater remediation, geological carbon sequestration, and hydrocarbon exploration. A study was undertaken to determine the effects of Mg2+ concentration on CaCO3 crystal morphology, precipitation rate, and porosity occlusion under flow and mixing conditions similar to those in subsurface aquifers. This was accomplished by promoting CaCO3 precipitation through the mixing of two solutions flowing parallel to each other in a microfluidic pore structure, containing uniform concentrations of dissolved Ca2+ and carbonate (CO32−), and systematic variations in the concentration of Mg2+. Raman spectroscopy indicates that all three polymorphs of CaCO3 (calcite, aragonite, and vaterite) were present under all experimental conditions. Coordinated brightfield imaging results show the morphology of calcite with increasing Mg2+ progressed from blocky and dogtooth approximately 10–80 μm in size, to anhedral spheroidal approximately 5–30 μm in size. The morphology of aragonite with increasing Mg2+ progressed from shrubs and fuzzy dumbells to spheroidal, and the size increased from approximately 5–60 μm to 20–200 μm. Recrystallization was observed in all experiments, but more so at low Mg2+, in which many small microcrystals dissolved and re-precipitated as one or a few larger calcite crystals. Analysis of brightfield images indicates calcite is the most abundant polymorph under all conditions. However, the area of pore space with aragonite increased from <5% when no Mg2+ was present to >20% at the highest Mg2+ concentration. The initial apparent precipitation rate of mineral polymorphs with no Mg2+ present was 2.5 times greater than when 40 mM Mg2+ was added, and large (20–200 μm) aragonite crystals formed primarily near to and below the center mixing zone with increasing Mg2+ concentration. Pore-scale modeling results are consistent with experiments, and indicate that all three polymorphs are thermodynamically favorable, with calcite and aragonite being the most favorable and having similar saturation ratios (SR > 100). The influence of Mg2+ on mineral precipitation rates is consistent with previous studies showing that calcite precipitation rates decrease with increasing Mg2+ concentrations. The precipitation of aragonite below the center-mixing zone is not predicted by thermodynamic SRs, but is consistent with the literature and our modeling results showing aragonite precipitation is kinetically more favorable in regions with higher Mg2+/Ca2+ ratios. Hence, both thermodynamic and kinetic constraints affect precipitation rates, the distribution of mineral polymorphs, and the corresponding extent of porosity occlusion. A tracer study demonstrated that mineral precipitation along the center-mixing zone under all experimental conditions led to substantial pore blockage. Imaging results suggest that with increasing Mg2+ concentration, slower crystal growth rates will increase the time period before pore blockage occurs, and the transition to more spherical and larger aragonite crystals below the center mixing line will increase pore occlusion and decrease mixing. Hence, understanding how Mg2+ affects calcium carbonate precipitation is very important for predicting mixing and reactive transport in subsurface reservoirs.