In this work, a sequential injection methodology for monitoring nitrite and nitrate in estuarine waters without any previous treatment is described. The developed system was applied to the measurement of nitrite and nitrate in estuarine waters of three rivers in the NW Portugal, allowing an automatic, fast (ca 60 h-1) and precise method (relative standard deviation lower than 2%). The procedure was based on the reaction between nitrite, sulfanilamide and N-(1-naphthyl)-ethylenediamine dihydrochloride (N1NED), whereas the determination of nitrate resulted from its reduction to nitrite, using an in-line cadmium column, followed by the same reaction. The samples were collected in three locations for each river (Douro, Cávado and Ave) covering the lower, middle and upper section of the estuaries. Despite the presence of a salinity gradient, this parameter showed no interference in the accuracy of the determinations. The results obtained for the described method for nitrite were statistically comparable to those obtained by the reference procedure. For the determination of nitrate, recovery tests confirmed that the sequential injection methodology provided good quality results.