In the present article the effects of Zn(II) on Botryococcus braunii in terms of growth and the photosynthesis-respiration metabolism and the ability of this microalgae to remove zinc present in wastewaters is described. The photosynthetic and respiration rates are affected by increasing metal concentration in solution, and therefore B. braunii growth rate decreases to a half, nevertheless the maximum value of biomass reached (770 ± 40 mg l−1) is the same and the biomass remains viable throughout the range of concentrations studied (0–80 mg l−1). B. braunii exposed the ability to reverse the acidic conditions of the medium, showing a pH increase from 5.2 till values above 8.0 favoring the precipitation of different zinc compounds. Zn(II) specific removal increases along with initial metal concentration. The net adsorption capacity was determined, and the Freundlich, Langmuir and Hill models were applied. The stoichiometric relationship between H+ release and zinc uptake in slightly acidic conditions is 1:1, and the adsorption kinetics follows a pseudo-second order model. The amount of metal removed increase when metabolic processes are involved. Removal of Zn with successive additions was achieved along 200 days, reaching a value of zinc removal of 3.4 g g−1. The remediation of heavy metals (zinc, nickel and copper) and nitrates present in a leachate obtained from a bioleaching process was successfully performed. The present work represents a new approach on the biotechnological potential of B. braunii to grow in acidic conditions and to remove zinc, while differentiates passive adsorption from metabolically active remediation.