A portable, wireless system capable of in situ reagent-based colorimetric analysis is demonstrated. The system is based on a reconfigurable low cost optical detection method employing a paired emitter detector diode device, which allows a wide range of centrifugal microfluidic layouts to be implemented. Due to the wireless communication, acquisition parameters can be controlled remotely and results can be downloaded in distant locations and displayed in real time. The stand-alone capabilities of the system, combined with the portability and wireless communication, provide the flexibility crucial for on-site water monitoring. The centrifugal microfluidic disc presented here is designed for nitrite detection in water samples, as a proof of principle. A limit of detection of 9.31 ppb, along with similar coefficients of correlation and precision, were obtained from the Centrifugal Microfluidic Analysis System compared with the same parameters measured using a UV-Vis spectrophotometer.