This work describes the development of a sequential injection system for the ammonium determination in transitional and coastal waters with a wide salinity range. Estuarine waters are rather complex matrices as their characteristics change considerably along the salinity gradient, as well as the ammonium levels. The developed system effectively solves these issues by converting ammonium into ammonia and using a gas diffusion unit (GDU) for matrix removal. The ammonium determination in a wide quantification range (0.1–5.0 mg L−1) was obtained with small changes in the protocol sequence and was applied, not only to estuarine samples, but also well water samples (low salinity) and coastal waters (higher salinity). Spectrophotometry was the chosen detection system to measure the absorbance change in the bromothymol blue acid base indicator caused by the diffusion of ammonia through the GDU. Additionally, the developed system used a green chemistry approach, as there was no indicator reagent consumption per determination, still maintaining a good precision (relative standard deviation lower than 2%) and a low detection limit, 27 μg L−1 (1.5 μM).
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