We investigated about the utilization improvement of the PDMS and fluoropolymers by mutual application in environmental analysis. We were conducted the direct fluorination with mild condition on the PDMS films and analyzed its surfaces before and after fluorination. The results of FTIR and SEM analysis on the PDMS films showed that the film surfaces were fluorinated without irreversible deformation by the fluorination. During the fluorination, the measured contact angles of water and several alcohols on the PDMS films decreased with time and that of most alcohols decreased to 0 after 30 minutes. The surface energy of fluorinated PDMS films has increased by 2 times. Also, we investigated the influence factors on the change of permeation rate of water through PDMS tubes with time. It was observed that the change of permeation rate of water through PDMS tube was affected by temperature, water phase and spatial distribution of water. From these results, we could verify the principal causes of the decrease of permeation rate of water through PDMS tube with time and proposed a new experimental setup for reducing the variation of permeation rate of water less than 2%.