We report a microfluidic paper based analytical device implementing ion concentration polarization (ICP) for rapid pre‐concentration of Escherichia coli in water. The fabricated device consists of a paper channel with a Nafion® membrane and in‐built micro wire electrodes to supply electric voltage to induce the ICP effect. E. coli cells were stained with SYTO 9 and fluorescence was used as a sensing method. The device achieved high concentration factor up to 2 × 105 within minutes. The effect of total ion concentration, on ICP and fluorescence intensity was studied. The reported device and method are suitable and effective for detection of E. coli during ballast water quality monitoring, coastal water quality monitoring where high salinity water is present.