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Previous heat transfer studies of nanofluids have shown that suspended nanoparticles can affect thermal properties within a fluid and furthermore can affect surface roughness by depositing on a heater surface. Pool boiling studies of nanofluids have demonstrated either enhanced or diminished heat transfer, yet have been unable to distinguish the contributions of increased surface roughness and suppression of bubble transport by suspended particles because they have used base fluids on a clean boiling surface as a comparison. We resolve this uncertainty by studying the boiling performance of a surface exposed to a series of boiling tests that alternate between water and a water-based nanofluid with suspended 40 nm ZnO nanoparticles. We find that the performance for the water tests increases significantly, showing a 62% enhancement after four cycles. This increase correlates well with a surface roughness model for boiling that uses atomic force microscopy-measured surface data to quantify the layering of nanoparticles in intervening nanofluid boiling tests. We find that the performance of the ZnO nanofluid initially shows a 24% enhancement versus water on a clean (unroughened) surface, but then steadily declines in later tests as nanoparticle layering occurs, showing a measured trend that is opposite that of water. We ascribe this decrease to the suppression of bubble formation and motion by the suspended particles. The results demonstrate that the effect of increased surface roughness due to nanoparticle layering can be twofold, greatly enhancing boiling for the base fluid and slightly decreasing performance for the nanofluid.