This paper reports an alternating current (AC) thermal flow sensor, based on the 3ω method, capable of measuring fluid flow in stacked microfluidic channels and through separating membranes. The measurement concept is tested in a triple-layer polydimethylsiloxane (PDMS) device containing two parallel channels separated by a membrane. A 3ω element integrated into the bottom channel was used to determine the flow direction and magnitude in both channels. Our results show that the phase of the temperature wave is linked not only to fluid velocity, but the physical dimensions of the channel, thus providing a novel non-contact tool to probe fluid flows.