Nanoclusters of two well-known tetrahedrally coordinated systems, (SiO2)N silica and (H2O)N water, are compared in the size range N = 8−26 with respect to energetic stability and T-atom topology (where T = Si and O, respectively). Because of the similar cage-forming tendencies of both systems in a number of bulk phases (e.g., clathrates), we focus on clusters with an even number of T-atoms for which cluster structural decomposition into a union of convex polyhedra (i.e., face-sharing cages with T-atom-vertices) is always possible. For (H2O)N, in the range N = 8−24, the even-N ground-state clusters are almost exclusively formed from face-sharing cubes and pentaprisms of T-atoms. We show that (SiO2)N clusters having the same T-atom topology as these prismatic water clusters are also low in energy (per SiO2 unit with respect to the corresponding lowest energy (SiO2)N cluster), and have the same groundstate structure for N = 12. Along with similarities, an important difference is discussed, namely that, rather than a converging tendency for the two systems to have similar prismatic topologies with increasing size, for (H2O)N at N = 24, self-solvating amorphous clusters compete strongly with the prismatic ground states, becoming ground states themselves for N > 24. Contrary to this shift in water cluster structural preference, (SiO2)24 clusters with the same T-atom topology as the amorphous (H2O)24 clusters are found to be high in energy with respect to both the (SiO2)24 ground-state and (SiO2)24 prismatic isomers. We discuss possible reasons for the existence and eventual breakdown of the topological analogy between (H2O)N and (SiO2)N nanoclusters with relation to the different bonding characteristics in each system.