In this study, the air–water two phase flow behavior in PEM fuel cell parallel channels with porous media inserts was experimentally investigated using a self-designed and manufactured transparent assembly. The visualization images of the two phase flow in channels with porous media inserts were presented and three patterns were summarized. Compared with the traditional hollow channel design, the novel configuration featured less severe two phase flow mal-distribution and self-adjustment to water amount in channels, although a higher pressure drop was introduced due to the porous media inserts. The dominant frequency of pressure drop signal was found to be a diagnostic tool for water behavior in channels. The novel flow channel design with porous media inserts may become a solution to the water management problem in PEM fuel cells.