The effect of nanoroughness on contact angles and pinning is investigated experimentally and numerically for low-energy surfaces. Nanoroughness is introduced by chemical vapor deposition of tetraethoxysilane and was quantified by scanning force microscopy. Addition of a root-mean-square roughness of 2 nm on a flat surface can increase the contact angle after fluorination by a semifluorinated silane by up to 30°. On the other hand, nanoroughness can improve or impair the liquid repellency of superhydrophobic surfaces that were made from assembled raspberry particles. Molecular dynamics simulations are performed in order to gain a microscopic understanding on how the length and the surface coating density of semifluorinated silanes influence the hydrophobicity. Solid-liquid surface free energy computations reveal that the wetting behavior strongly depends on the density and alignment of the semifluorinated silane. At coating densities in the range of experimental values, some water molecules can penetrate between the semifluorinated chains, thus increasing the surface energy. Combining the experimental and numerical data exhibits that a roughness-induced increase of the contact angle competes with increased pinning caused by penetration of liquid into nanopores or between neighboring semifluorinated molecules.