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High-frequency field nutrient analyzers offer a promising technology to solve time-consuming and laborious sampling problems in dynamic and complex river−estuarine− coastal ecosystems. However, few studies on the simultaneous underway analysis of five key nutrients (ammonium, nitrite, nitrate, phosphate, and silicate) in seawaters are available because of the limitations of the technique. In this study, a state-of-the-art autonomous portable analyzer for the shipboard analysis of nutrients in the environment of varied salinities and concentration ranges was reported. The analyzer consisted of compact hardware that was well suited for shipboard deployment with minimal maintenance. Moreover, a novel LabVIEW-based software program was developed, containing additional functions such as automated calibration curve generation, autodilution of high-concentration samples, and a user-friendly interface for multiparameter analysis using a single instrument. After the optimization of chemical reactions and work flow chart, the analyzer exhibited low limits of detection, a large linear range with automated dilution, and relative standard deviations of less than 2% (n = 11). Compared to other flow-based techniques, this analyzer is more portable and consumes less reagent with an autonomous data processing function and applicability within a broad salinity range (0−35). The analyzer was successfully applied for real-time analysis in the Jiulong River Estuary−Xiamen Bay with excellent on-site accuracy and applicability. The relationship between high spatial resolution nutrient concentrations and salinities showed very different patterns in estuarine and coastal areas, indicating the benefit of using an underway automated analyzer for chemical mapping in a dynamic environment.