Microfluidic technology permits the miniaturization of chemical analytical methods that are traditionally undertaken using benchtop equipment in the laboratory environment. When applied to environmental monitoring, these "lab-on-chip" systems could allow high-performance chemical analysis methods to be performed in situ over distributed sensor networks with large numbers of measurement nodes. Here we present the first of a new generation of microfluidic chemical analysis systems with sufficient analytical performance and robustness for deployment in natural waters. The system detects nitrate and nitrite (up to 350 μM, 21.7 mg/L as NO(3)(-)) with a limit of detection (LOD) of 0.025 μM for nitrate (0.0016 mg/L as NO(3)(-)) and 0.02 μM for nitrite (0.00092 mg/L as NO(2)(-)). This performance is suitable for almost all natural waters (apart from the oligotrophic open ocean), and the device was deployed in an estuarine environment (Southampton Water) to monitor nitrate+nitrite concentrations in waters of varying salinity. The system was able to track changes in the nitrate-salinity relationship of estuarine waters due to increased river flow after a period of high rainfall. Laboratory characterization and deployment data are presented, demonstrating the ability of the system to acquire data with high temporal resolution.