We present the design and development of a continuous flow, semi-autonomous, quantitative Polymerase Chain Reaction (qPCR) system. This battery-powered system operates under programmable control and is able to detect many different primer probe combinations as is required for environmental analyses. Our design focuses on a system with re-usable components for low levels of consumables, automated fluid handling and low power consumption. It also maintains user control over essential parameters including sample volume, temperature, and cycle time. We use a two-phase emulsion system connected to a continuous flow, two-temperature zone cylindrical thermocycler. The fluorescence from each channel is excited using an LED coupled through a fiber optic bundle and emission detected using optical fiber coupling to a 64 channel PMT. Data collection and quantitative PCR analysis is performed using a laptop computer. This platform can be transported for in-situ field applications.