Microbial Induced Calcium Carbonate Precipitation (MICP) influenced by biofilm metabolism in the subsurface can be exploited for a variety of engineered applications encompassing geotechnical ground improvement, environmental bioremediation, and hydraulic barriers. A reactive transport model was developed to determine the effects of controlling factors in terms of treatment protocols and experimental methods. Six column tests were calibrated and a range for the key parameters was determined. Fifteen key parameters of MICP reactive transport model were assessed in four categories (microbial activity and attachment, sample preparation, treatment protocol, and experiment dimensions). The results emphasized the effects of three main factors of microbial activity, microbial attachment process, and number of treatment (among all 15 assessed parameters) on the calcium carbonate (CaCO3) precipitation content and distribution. An increase in specific ureolysis rate (Ku) and attachment rate coefficient (Kat) by two orders of magnitude improves average CaCO3 by up to 13% and 6%, respectively with non-uniformity (COV) increase of 16%. Higher flow rates and solution concentrations contribute to more uniform CaCO3 distribution. The constant attachment rate model is useful to yield the CaCO3 precipitation profiles but more accurate models are needed to capture exact distribution. Post-treatment hydraulic conductivity, porosity and attached biomass were assessed.