Thirty strains of microfungi and amylolytic yeasts were screened for production of microbial biomass protein (MBP) and water reclamation from starch processing wastewater (SPW). Three species and six strains of microfungi Aspergillus oryzae, Rhizopus oligosporus and Rhizopus arrhizus showing high enzymatic activities on SWP were selected under non‐aseptic growth conditions. In 20 h submerged cultivation the selected strains had a high capacity to enzymatically hydrolyse more than 93% of the starch and produce 4.3–5.6 g dm−3 of dry biomass at a specific biomass growth rate from 0.05 to 0.12 h −2. The fungal biomass contained crude protein ranging from 37.5 to 49.8% of dry biomass. The pellet and flocculated biomass products were easily harvested by simple filtration or sedimentation. After these processes, 76–88% of total organic carbon (TOC), 85%–92% of chemical oxygen demand (COD) and 95% suspended solids in SPW were removed, and the treated water was reusable for farm irrigation. Typical pretreatment processes including hydrolysis, sterilisation and nutrient supplementation were unnecessary.