The ongoing and increasing worldwide demand for fish has caused a steady increase in aquaculture production during the last decades. This emphasizes the importance of farming systems with a low ecological footprint, like recirculating aquaculture systems (RAS), which are an alternative to traditional open systems. Furthermore, implementing microalgae treatments in RAS, sustainable water management and low discharge of concentrated wastewater could be achieved, allowing its reuse in the system. The influence of three factors on microalgae treatment efficiency in RAS water were studied: i) microalgae species (Chlorella vulgaris, Tetradesmus obliquus), ii) water pre-treatment (sterile filtration), and iii) sampling location within the RAS (e.g. from fish tank, after UV-disinfection, etc.). To this end, fully factorial, replicated cultivations were carried out in 100-ml flasks, and nutrient removal, microalgae growth, and density of bacteria and protozoa were measured for up to 18 days. Results show that both species are able to grow in RAS water and effectively remove nutrients in it, yet their performance depended greatly on water quality. In sterile RAS water, growth and nutrient removal efficiency of C. vulgaris surpassed that of T. obliquus. In non-sterile RAS water, the pattern reversed because of grazing proto- zoa. The location of sampling within the RAS had no discernible effect on microalgae growth or nutrient removal efficiency. The results confirm that a microalgae-based technology to treat and valorise RAS water is technically feasible, yet caution that inferences made can be reversed depending on the choice of the species and the pre- treatment of the RAS water prior to cultivation.