This study examined the effect of surface roughness on the pool boiling heat transfer coefficient of pure water and water-alumina nanofluid with 0.1% and 0.01% volume concentration using computational fluid dynamics on the surface of a stainless-steel cylinder. The effect of nanoparticles was checked by averaging the thermophysical properties in the equations of the flow field with boiling. Simulations were performed for initial surface roughnesses from 0.1 to 0.8 µm. Furthermore, the presence of nanoparticles would make their deposition on the heated surface and change the surface properties. Thus, once again simulations were performed for roughness with the same values but because of the deposition of nanoparticles. In doing so, two separate equations were used for the nucleation site density parameter. Ultimately, the results obtained from both types of roughness were compared. The results indicated that with an increase in the roughness, the boiling heat transfer coefficient increased. Further, at the same roughness, the boiling heat transfer rate of the deposited surface decreased for nanofluid of 0.01% vol and increased for nanofluid of 0.1% vol compared to the non-deposited surface. For pure water at 0.8 µm roughness, the sediment improved heat transfer but it reduced heat transfer for 0.4 µm and lower roughness.