Many microfluidic systems have been designed, fabricated and applied to a variety of different analyses in silicon. In recent years attention has turned to polymer fabrication for a number well-documented reasons. The three major advantages of polymer fabrication that have sparked this trend include rapid prototyping, the availability of cheap starting materials and the abundance of polymers with different chemical, physical, electrical and mechanical properties to suit every application. Laser micro machining was chosen for the fabrication of the microfluidic components in this prototype system presented here and polymethyl methacrylate, PMMA as the polymer substrate. The three-layered microfluidic chip was bonded with an applied force at elevated temperatures and leak-free fluidic interconnects were designed. The chosen application for this device is a simple stopped flow measurement in the determination of phosphorus in natural waters. The colorimetric method chosen was based in the formation of the yellow vanadomolybdophosphoric heteropoly acid complex in the presence of inorganic orthophosphate ion in water. Optical detection below 400 nm was achieved with a UV-LED as light source. The optical alignment of the UV-LED through the microfluidic chip at the optical cuvette and the overall integration of the optical components into the manifold were described here.