We report a study of silicate oligomerization in water solution in the presence of counterions (Li+ and NH4+) using continuum kinetic Monte Carlo (kMC). The parameters required for kMC are obtained from density functional theory (DFT) calculations. Formation of cyclic trimers (3-rings) and branched tetramers have been reported by using several models, including DFT in the gas phase, DFT with COSMO treating the solvent, Car–Parrinello simulations with explicit water molecules, and also experimental results. However, the results are substantially different. Moreover, in many other studies, no branched tetramer was observed. In this work, the silicate oligomerization from monomer to 3-ring and branched tetramer, and the roles of counterions in these processes, are discussed in detail. The presence of counterions is found to influence the oligomerization rate and selectivity, and a structure-directing role of counterions is found. Results reveal that Li+ favors formation of branched tetramers over 3-rings, whereas NH4+ directs the formation of 3-rings.