Nanostructured copper oxide thin films were deposited on soda lime glass substrates by reactive radio frequency (RF) magnetron sputtering using pure Cu target. The effect of oxygen (O-2) partial pressure (5-50%) on physical properties of deposited films were investigated. The XRD analysis indicates the cubic structure of Cu2O changes to monoclinic CuO as a function of increasing O-2 pressure. The Raman spectroscopy results further confirmed the phase variations of Cu based oxide films. Morphological analysis showed that the deposited films are highly uniform with nano gravels and agglomerated nano flake like structures for Cu2O and CuO thin films respectively. The surface roughness of the films decreases from 2.05 to 1.07 nm by increasing O-2 pressure. X-ray photoelectron spectroscopy confirmed the binding energy variation in the oxidation state of the films. The optical band gap of deposited Cu2O is 2.12 eV, while that of CuO varies in the range of 1.79-1.82 eV. Hall effect measurement revealed that all the films exhibit p-type conductivity. The photocatalytic activity studies of as-deposited films have been carried out with different organic pollutants such as methylene blue, methyl orange and ciprofloxacin under solar irradiation. The Cu2O thin films exhibited higher degradation efficiency than CuO films under identical conditions. The mechanism of photocatalytic activity of copper oxide thin films is explained.