Display omitted •A continuous-flow microalgal-bacterial granular tubular reactor was developed.•Daytime was favorable for ammonia removal while nighttime for nitrate removal.•Phosphate-P removal was highly reliable on the weather condition.•Nitrite-N maintained high removal efficiency of over 99% under varied conditions.•Superb nitrite removal relied mainly on nitrite reduction instead of denitrification. This study developed a continuous-flow non-aerated microalgal-bacterial granular tubular reactor for aquaculture wastewater treatment under natural day-night conditions. Results showed that daytime was favorable for ammonia removal while nighttime for nitrate removal. Over 99% of nitrite-N could be removed over the day-night cycles at a hydraulic retention time of 6 h. However, the phosphorus removal was found to be sensitive to the weather condition, ranging from 35.0% to 96.6%. It was also observed that dissolved oxygen produced by microalgae in daytime was sufficient for creating a 6-h aerobic condition in nighttime for sustaining heterotrophic activity. Chlorella and Leptolyngbya were identified as the most abundant algae related to weather changes. Metagenomics analysis revealed that the high nitrite removal relied mainly on nitrite reduction. These experimental findings offer new insights into the non-aerated microalgal-bacterial granular sludge for environmentally sustainable aquaculture wastewater treatment.