The use of lagoons with floating aquatic plants for the treatment of a polluted urban river with recovery of Pistia stratiotes biomass was investigated. A first group of experiments was performed during spring, comparing three different media: synthetic wastewater (SWW), water from the Sordo River (WSR), and WSR amended with fertilizer (WSR + F). The second and third experiments were performed during summer and winter, respectively, using only WSR. During spring, the productivity in WSR and WSR + F was similar between them and significantly higher compared to the one observed in the SWW: 0.949 versus 0.379 g dry weight (dw) m−2 day−1, respectively. During summer, the productivity in the WSR was similar to the one observed in spring but significantly different to the one registered in winter: 0.946 versus 0.347 g dw m−2 day−1. During spring and summer, the uptake rate of ammonium nitrogen was significantly higher compared to the one registered for nitrate, although in winter there were no differences between such rates. For phosphates, the removal percentage was similar in spring and winter (96.25 and 99.1%, respectively). It was concluded that this system serves a dual purpose, treating water from a polluted river effectively and producing high biomass yield during spring and summer.