An flow-injection system is described for the in-situ determination of nutrient concentrations in rivers and ocean waters. In estuarine and coastal waters, significant interferences may be caused by temperature and salinity variations. Therefore, we used a dual wavelength detector to measure simultaneously the reference and sample signals. The device has been used to measure spatial and temporal variations of nitrite and nitrate concentrations in coastal waters exhibiting strong salinity variations (Bay of Brest and Iroise Sea, France). Our original detection system coupled with flow-injection analysis (FIA) allows high-frequency measurements (40 samples per hour), very good precision (1%) and a low detection limit (0.45 mu M NO3). The device can work up to a depth of 300 m, within a temperature range of 2 to 35 degrees C, and with salinities varying from 0 to 35. The dynamic range (0-150 mu M NO3) can be adapted to the expected concentrations of the study area by using flow cells with various path lengths. Intercalibration with samples collected by conventional means and analysed with a spectrophotometric reference method at the laboratory showed a good agreement between both methods (1.3%).