An in situ, atomic force microscopy-(AFM-)-based experimental approach is developed to directly measure the kinetics of silica nucleation on model biosubstrates under chemical conditions that mimic natural biosilica deposition environments. Relative contributions of thermodynamic and kinetic drivers to surface nucleation are quantified by use of amine-, carboxyl-, and hybrid NH3+/COO--terminated surfaces as surrogates for charged and ionizable groups on silica-mineralizing organic matrices. The data show that amine-terminated surfaces do not promote silica nucleation, whereas carboxyl and hybrid NH3+/COO(-)substrates are active for silica deposition. The rate of silica nucleation is similar to 18x faster on the hybrid substrates than on carboxylated surfaces, but the free energy barriers to cluster formation are similar on both surface types. These findings suggest that surface nucleation rates are more sensitive to kinetic drivers than previously believed and that cooperative interactions between oppositely charged surface species play important roles in directing the onset of silica nucleation. Further experiments to test the importance of these cooperative interactions with patterned NH3+/COO-substrates, and aminated surfaces with solution-borne anionic species, confirm that silica nucleation is most rapid when oppositely charged species are proximal. By documenting the synergy that occurs between surface groups during silica formation, these findings demonstrate a new type of emergent behavior underlying the ability of self-assembled molecular templates to direct mineral formation.