This research evaluated the influence of organic matter (OM) and CO2 addition on the bioremediation potential of two microalgae typically used for wastewater treatment: Chlorella vulgaris (CV) and Scenedesmus almeriensis (SA). The heavy metal (HM) removal efficiencies and biosorption capacities of both microalgae were determined in multimetallic solutions (As, B, Cu, Mn, and Zn) mimicking the highest pollutant conditions found in the Loa river (Northern Chile). The presence of OM decreased the total biosorption capacity, specially in As (from 2.2 to 0.0 mg/g for CV and from 2.3 to 1.7 mg/g for SA) and Cu (from 3.2 to 2.3 mg/g for CV and from 2.1 to 1.6 mg/g for SA), but its influence declined over time. CO2 addition decreased the total HM biosorption capacity for both microalgae species and inhibited CV growth. Finally, metal recovery using different eluents (HCl, NaOH, and CaCl2) was evaluated at two different concentrations. HCl 0.1 M provided the highest recovery efficiencies, which supported values over 85% of As, 92% of Cu, and ≈ 100% of Mn and Zn from SA. The presence of OM during the loaded stage resulted in a complete recovery of As, Cu, Mn, and Zn when using HCl 0.1 M as eluent.