Agricultural, domestic and industrial activities contribute in releasing several organic and inorganic substances into the water streams that result in environmental pollution. Biological treatment of industrial and domestic wastewater using Activated Sludge Nutrient Removal (ASNR), the conventional process, is well known; however, it is relatively expensive due to the requirement for high energy inputs. Microalgal applications have been gaining interest as they offer potential cost-effective measures for the treatment of wastewater in the peri-urban and rural areas. Such systems provide an interesting tertiary biological treatment method where valuable biomass is produced with simultaneous uptake of nutrients such as nitrogen and phosphorous with reduction in coliform bacteria, heavy metals, chemical and biochemical oxygen demand (COD & BOD) and the removal/degradation of xenobiotic compounds etc. This paper provides a systematic review on the current microalgal applications (phycoremediation) for wastewater treatment with advanced information on their role towards nutrient recovery and energy (biogas) production under the third generation biorefinery concept. The use of advanced algal pond systems for wastewater treatment including pollutant degradation, microalgal cultivation and employing such facilities for biogas production in view of technology applications is emphasized. This inter-linked network indicating microalgal role into the Nutrient-Energy-Wastewater nexus with future directions and concluding remarks are discussed.