We demonstrate a microfluidics-based fluorescence detection device where the filters, source, detector, and electronically controlled valves are embedded into a Polydimethylsiloxane (PDMS)-based microfluidic chip. The device reported here has been specifically designed for chlorophyll a fluorescence sensing in autonomous systems, such as oceanic applications. In contrast to a monolithic approach, the modular approach made the fabrication of this device simpler and cheaper. For fluorescence detection, an InGaN/GaN LED is used as the excitation source to specifically excite chlorophyll a; a metal-dielectric FabryPerot filter was used to extinguish out-of-band excitation. A simple Si photodiode is used as detector and provided with a thermally evaporated CdS emission filter to block the excitation source. This filter combination provides an excellent solution to the difficult problem of combining high-rejection excitation and emission filters in an integrated thin-film format. Furthermore, the metal-dielectric filter provides a much broader angular response than a comparable multilayer Bragg mirror, which is a key advantage in the integrated format. We use a novel paraffin wax-based valve design affords low power single-use actuation, between 0.5 and 1 J per actuation and withstands 0.6 bar differential pressure, which provides better performance than its previously reported counterparts. The remote valve-controlled operation of the fluorescence detection system is demonstrated, illustrating the measurement of a chlorophyll a solution, with a detection limit of 340 lM and subsequent valve-controlled flushing of the measurement reservoir.