A new in-situ instrument to simultaneously and rapidly detect the nitrates and nitrites of water is presented based on the sequential injection analysis (SIA) and spectrophotometer. The optimal time and injection speed for incomplete chemical color reaction of nitrite with reagent and deoxidization efficiency of cadmium column on changing nitrate to nitrite were studied and selected to obtain the rapid detection speed (the detection time for a sample can be as short as 5 mins for nitrates and 4 min for nitrites) of nitrates and nitrites in situ. In this instrument, the liquid-core waveguide (LCW) was adopted to replace the quartz cuvette as the colorimetric cell to obtain a relatively low detection limit(nmol·L-1) and very small sample consumption, and all water sample was filtered before sample injection and measurement. These measures make this in-situ detection instrument have the advantages of complete automation, very quick detection speed, low weight and power consumption, and good versatility and extensibility. Only by replacing the reagent or LCW, it also can be used to measure the trace element of water or other nutrition elements such as phosphate, silicate etc, in different sea areas in profile or fixed-point.