Microorganisms have long been thought to impact CaCO3 precipitation, but determining the extent of their influence on sediment formation has been hampered by our inability to obtain direct experimental evidence about mineral formation processes in natural environments. We address this problem by conducting kinetic experiments within a modern terrestrial carbonate spring to determine aragonite precipitation rates and to quantify the relative influences of aragonite saturation state (Ωa), microbial biomass concentration and microbial viability on CaCO3 mineralization in advection-dominated transport regimes. At an Ωa value consistent with modern seawater (3.63 ± 0.09), our controlled in situ kinetic experiments show that: (1) the natural steady-state aragonite precipitation rate is more than twice that determined when microbial biomass on the aragonite mineral surface is depleted by 0.2 µm filtration; and (2) inhibiting microbial viability with ultraviolet (UV) irradiation has no significant effect on the mean precipitation rate. Furthermore, our modeling of the CaCO3 precipitation process, which uses the empirical crystal growth rate expression and additional in situ kinetic measurements, reveals that reducing biomass concentrations by 45% can decrease the empirical rate constant by more than an order of magnitude. These findings strongly suggest that microorganisms catalyze CaCO3 precipitation in advection-dominated systems and imply that changes in carbonate mineralization rates may have resulted from changes in local microbial biomass concentration throughout geologic history.