The continous flow autoanalyzer is an instrument commonly used for nutrient analysis in coastal laboratories and oceanographic vessels. The determination of micronutrient concentrations (ammonium, nitrites, nitrates, silicates and phosphates) makes it necessary to evaluate precisely how variables can affect this measure. In this sense, salinity is a parameter which must be considered, due to its wide range of variation (0–36) in estuarine ecosystems. In this work, the effect of salinity on nutrient (ammonium, nitrites, silicates and phosphates) determination is analyzed. The results show that salinity does not affect the measure of nitrites and phosphates, whereas ammonium and silicates are affected. Practical considerations of nutrient measurement with samples of different salinities are pointed out.