The use of microalgae-bacteria consortia for effluent treatment is an emerging and promising technology that has seen continuous development over the past few decades. To optimize and efficiently apply this technology, it is essential to understand the biology surrounding these systems, in which microalgae, heterotrophic bacteria, and nitrifying bacteria play a fundamental role. These relationships are governed by environmental parameters (light, temperature) and operational parameters (pH, culture deep, air, and CO2 injection) used in treatment systems. Therefore, understanding the influence of these parameters while achieving proper control strategies and automation presents a significant challenge. In southern Spain, in Almería, at the IFAPA Research Center in collaboration with the University of Almería, pilot-scale bioreactors of different designs and sizes have been operating for years to treat wastewater. Specifically, this case study focuses on the study of two identical 80 m2 raceway reactors operated continuously, one with wastewater and the other with a mineral medium based on chemical fertilizers. Although the results are promising, this technology still faces challenges, such as the complete removal of organic matter present in these effluents. In the future, coupling this technology with others, such as microbial fuel cells, is proposed to not only treat wastewater but also produce valuable biomass and energy.