Biofouling is a serious concern for the materials that are in contact with seawater or brackish water. Superhydrophobic (SHP) surfaces have the potential to lower fouling. Although good progress is made on the design of SHP surfaces, the long-term antifouling performance of SHP surfaces is still a major concern. We report the effect of substrate material, hierarchical surface features, chemistry, and the nature of bacteria on the long-term antifouling properties of superhydrophobic for the first time. Three different superhydrophobic coatings on aluminum, Cr-Mo steel, and Ti substrates were studied in a seawater bacterial consortium. Silane based SHP Al with a water contact angle (WCA) ~170 ± 1.5°, cerium myristate based SHP Cr-Mo of WCA ~ 162 ± 2.4° and stearic acid based SHP Ti of WCA ~168 ± 3.3° were prepared by dip coating, electrodeposition, and rapid breakdown anodization, respectively. After 120 h of exposure in seawater bacterial consortium, the cell viability reductions were three, two and one order in SHP Al, SHP Cr-Mo, and SHP Ti, respectively. The SHP Al samples possessed both micron-sized structures (~2 µm) along with nano-sized spherical particles (~ 57 nm). The quat silane-like structures gave better antibacterial resistance to SHP Al. The predominant bacteria present on bare Al,Ti, Cr-Mo and SHP Al, and Ti surfaces after exposure were Bacillus and Pseudomonas sp., whereas cocci bacteria was seen on the SHP Cr-Mo. After 240 h of exposure, a thicker biofilm was seen on the SHP Cr Mo surface due to the densely populated nanostructures of sizes comparable to cocci diameter, which was favorable for the cocci bacterial attachment. Though the average WCA followed the trend SHP Ti> SHP Al>SHP Cr Mo, the bacterial adhesion trend was SHP Ti> SHP Cr Mo> SHP Al, after 120 h of exposure. This suggests that wettability is not the only parameter determining the antifouling performance of an SHP coating but is also influenced by the surface charge density, surface roughness, stiffness, topography, and environmental variables such as fluid dynamics, bacterial motility, and size and morphology of bacteria. Both the surface morphology and the chemical nature were responsible for this reduced cell viability of the SHP Al surface. These findings not only provide new insights into the understanding of long-term biofouling of SHP surfaces but also would provide new directions in the design of robust SHP surfaces.