Monodisperse, bimetallic nanocatalysts, homogeneously supported on mesoporous silica nanoparticles, are demonstrated as highly active, reducing catalysts for rapid and selective nitrate transformation. For this, we finely controlled catalyst size and composition based on new synthesis strategies. Specifically, atomic clusters of Mreducing/Cu nanocatalysts (Mreducing = Pd, Pt) were optimized for nitrate reduction via subsequent Mreducing impregnation (Mreducing/Cu/Mreducing combinations). Reaction kinetics were observed to be affected by the ratio of Mreducing to Cu, for which Pd−rich Pd/Cu/Pd nanocatalysts showed better performance than Cu−rich analogs. Product selectivity (ammonium vs. nitrogen) was highly correlated with nanocatalyst morphology, with nitrogen gas (dominant) selectivity observed for relatively larger Pd particles. Lastly, MSN−Pd/Cu/Pd catalyst are highly stable in water, with no catalyst deterioration over multiple reactions (10 cycles), while maintaining consistently high reaction rates and N2 selectivity. Taken together, this study demonstrates the critical importnace of precise catalyst control and stability towards optimizing nitrate reduction processes.