The cultivation of microalgae or/and cyanobacteria in nutrient-rich wastewaters presents a significant opportunity for enhancing sustainability of tertiary wastewater treatment processes via resources/energy recovery/production. However, maintaining a monoculture in wastewater-media constitutes a significant challenge to be addressed, as a plethora of antagonistic and predating microorganisms exist is such media. In this regard, the present work assesses the efficiency of the low-cost wastewater substrate disinfection techniques of filtration, use of NaClO, H2O2 or Fe(VI), in terms of antagonistic or/and predating microbial species growth inhibition in Synechococcus elongatus PCC 7942 cultivations. Nitrates and phosphates removal rates were also experimentally assessed. The results showed that filter thickness has a greater effect on disinfection efficiency than that of filter’s pore size. Furthermore, the disinfection efficiency of Fe(VI), which was produced on-site by electrosynthesis via a Fe0/Fe0 cell, was greater than that of NaClO and H2O2. Filtration at ≤ 1.2 µm pore size coupled with chemical disinfection leads to unhindered S7942 growth and efficient nitrates and phosphates removal rates, at dosages of CT ≥ 270 mg min L−1 for NaClO and CT ≥ 157 mg min L−1 for Fe(VI). The coagulation action of Fe(III) species that result from Fe(VI) reduction and the oxidation action of Fe(VI) can assist in turbidity, organic compounds and phosphorous removal from wastewater-media. Moreover, the residual iron species can assist in S7942 harvesting and may enhance photosynthesis rate. Thus, the utilization of wastewaters for S7942 cultivation as tertiary treatment seems a promising and novel alternative to common nutrient removal processes that can reduce environmental footprint and operational costs of wastewater treatment plants.