BACKGROUND: The use of microalgae-bacteria systems is particularly attractive for wastewater treatment, and the generated biomass can be further used for methane production. The aim of this study was to evaluate the influence of the hydraulic retention time (HRT) on the organic matter, nutrient removal, settling properties and the biochemical methane potential using a granular microalgae-bacteria system in a high rate algal pond. RESULTS: The primary microorganisms present in the system were constituted by diatoms, green filamentous microalgae and bacteria. At 2 d of HRT the system showed the lowest performance while high chemical oxygen demand (COD) (>92%), ammonium (>85%) and phosphorus (up to 30%) removal was observed at 6 and 10 d of HRT. High settling velocities (up to 8 m h(-1)) were observed due to agglomerates and granules as dominant structures. The highest methane yield and production rates (348 mL CH4 g(-1) VS and 56 mL CH4 g(-1) VS d(-1)) were observed with the biomass obtained at 10 d of HRT. CONCLUSION: Flocs and granules were the dominant structures in the system. High settling velocities and low effluent total suspended solids concentrations were obtained at higher HRT. An inverse relationship between HRT and the biochemical methane potential was observed. (C) 2016 Society of Chemical Industry