A reactive transport model has been developed to simulate the bio-chemo-hydro-mechanical coupled process associated with soil improvement by Microbially Induced Calcite Precipitation (MICP) in shallow submerged conditions. Besides including the key processes of bacterial attachment and decay, urea hydrolysis, and CaCO3 3 precipitation, this study demonstrates the necessity to account for variable fluid density and associated gravity- driven flow, to select the appropriate boundary conditions by including the water adjacent to the sand as a separate domain and to include bacterial detachment. After fitting the parameters describing bacterial attachment, detachment, decay, and the reaction kinetics, the final precipitated calcium carbonate from the numerical simulations exhibits a decent agreement with the experimental results presented by Montoya et al. (2021) in terms of quantity and distribution pattern. However, still differences exist between the simulated and measured shear wave velocity (Vs) V s ) and its increment through multiple treatment cycles, which suggests a more complex coupling between porosity, hydraulic conductivity, small strain stiffness, and the type or pore habit and heterogeneity of the distribution of the precipitated CaCO3. 3 . The limitations of the model and directions for further development to capture the complexity of this coupled process are discussed.