This paper deals with biological treatment of malt house wastewater using algal-bacterial flocs. During three months of testing, optimisation of growth conditions and biomass separation leads to maximisation of biomass production, improved flocs settleability and increased pollutant removal efficiency while maintaining low energy demand. At a high food to microorganism ratio (0.16 to 0.29 kg BOD5 kg−1 TSS d−1), the biological oxygen demand (BOD5), chemical oxygen demand (CODCr), total phosphorus (Ptot) and total suspended solids (TSS) removal efficiencies were all higher than 90%. At a food to microorganism ratio of 0.06 kg BOD5 kg−1 TSS d−1, BOD5, CODCr, total nitrogen (Ntot), Ptot and TSS removal efficiencies of 99.5%, 97.6%, 91.5%, 97.8% and 98.4%, respectively, were achieved. The study also proved a strong dependence of removal efficiencies on solar radiation. The results suggest the algae-bacteria system is suitable for treatment of similar wastewater in locations with available land and sufficient solar radiation and temperature during the whole year.