The tertiary treatment using microalgae offers an attractive alternative to the removal of low but relevant concentrations of pharmaceuticals from domestic wastewaters. The removal of fluoxetine from aqueous solutions by living and non-living (lyophilized) Chlorella vulgaris was assessed. The determination of the pH at the point of zero charge, Fourier transmittance infrared analysis, and scanning electron microscopy were performed to characterize the microalgae biomass. Kinetic and equilibrium experiments were performed. The pseudo-second-order model described the kinetics of fluoxetine. The corresponding kinetic constants indicated that biosorption was faster onto non-living biomass than onto living biomass. The equilibrium results showed that the systems followed the Langmuir isotherm model. The maximum capacity of living microalgae (1.9 ± 0.1 mg·g−1) was slightly higher than the non-living microalgae (1.6 ± 0.2 mg·g−1). Living Chlorella vulgaris, free and immobilized in calcium-alginate, were also used to remove fluoxetine and nutrients (nitrogen and phosphorus) from treated municipal wastewater in a batch system. In both experiments, fluoxetine was completely removed within six days. The total phosphorus (TP) and total nitrogen (TN) removal efficiencies achieved for free and immobilized cells were, null and 65.0 ± 0.1%, and 86.2 ± 0.1% and 81.8 ± 3.1, respectively.