In this present research, a novel microwave hydrothermal method was applied to cotton fabrics to develop a superhydrophobic surface by rapid synthesis of aligned ZnO nanorods on the surface of the cotton fabric. A two-step approach was used to grow the ZnO nanorods. Firstly, the cotton fabric was coated by a seed layer of ZnO nanocrystals, synthesized using the microwave-assisted sol gel method. Secondly, the ZnO nanorods were grown rapidly on the seeded cotton fabrics using the microwave hydrothermal method. Moreover, a layer of non-fluorinated silane was applied on the as-grown nanorods to fabricate a superhydrophobic surface. Non-fluorinated silane was selected as it is less harmful to the skin than fluorinated silanes. The effect of the zinc nitrate hexahydrate (Zn(NO3)2·6H2O) concentration, reaction time and microwave power on the growth of ZnO nanorods was investigated in detail using scanning electron microscopy. The surface topography and roughness of the nanorods grown on the fabrics were studied using atomic force microscopy. EDS analysis and X-ray diffraction techniques were used to study the structural properties of the ZnO nanorods. The ultraviolet protection properties were investigated by a UV–Vis-NIR spectrophotometer. The ZnO nanorods grown on the cotton fabrics exhibited excellent UV blocking properties. A maximum UPF value of 114 was observed for the ZnO nanorods grown on the cotton fabric with 100 mM of zinc nitrate hexahydrate (Zn(NO3)2·6H2O). The superhydrophobic properties were examined based on contact angle and roll-off angle measurements, where a maximum water contact angle of 170.2° and a minimum roll-off angle of 1° were found for 25 mM of zinc nitrate hexahydrate. The ZnO-OTMS coated fabrics were evaluated for superhydrophobic durability against mechanical abrasion, laundering, chemical and UV action. Moreover, the ZnO-OTMS coated fabrics showed excellent potential for separation of floating and underwater oil layers or an oil–water mixture.