Wastewater represents an alternative source of nutrients in which to grow microalgae, whilst improving the quality of the wastewater, and reducing the downstream treatment required. However, commercialisation of microalgal cultures for such duties faces a number of challenges, predominantly high cost and low productivity. Suspended-solid reactors (ssPBR) can reduce the operational costs, while promoting attached and suspended microalgae growth. In the present study, a novel approach was developed by integrating microalgal wastewater treatment with carrier systems to favour the growth of both attached and suspended cells of T. obliquus. This study found that T. obliquus was able to uptake nutrients from municipal wastewater, achieving removals of 99.3–99.9 % NH3-N, 54.5–88.5 % PO43− and 92.8–94.5 % DTC. The addition of a 12.5 % volumetric fill ratio of carriers in ssPBRs produced higher microalgal cell productivity (1.2·106 ± 2.5·105 cell ml−1 d−1) than the control (4.3·105 ± 2.8·105 cell ml−1 d−1). MinION nanopore sequencing was conducted to assess the impact of microalgal and carrier treatment on wastewater bacterial communities. It was found not only that bacterial communities had changed after the treatment but also the ones attached differed from the ones suspended. Untreated wastewater was characterised by the abundance of sewer bacteria genera such as Aliarcobacter and Arcobacter, whilst, after treatment, microbial communities were characterised by the presence of photosynthetic freshwater (Limnococcus, Stanieria) and bioremediation-like bacteria genera (Pseudomonas, Rheinheimera). In conclusion, the addition of 12.5 % fill carrier ratio increased microalgal productivity, while stimulating changes in the algal microbiome, and creating distinctly different populations in the free and attached environments.