A biofilter reactor, to which is attached a large variety of microorganisms, can be employed to treat circulating water in an intensive aquaculture system. Some nitrogen-containing wastes, such as ammonium and nitrite, are toxic to the aquatic organisms. The removal rates of the nitrogenous wastes are regarded as indices for the efficiency of treatment by biofilters. In this study, a fungus that was characterized as being able to remediate multiple nitrogenous wastes was identified as Aspergillus niger NBG5. In a continuous fixed-slab reactor, the heterotrophic fungus utilized ammonium, nitrite, protein, and glucose simultaneously. The fungus assimilated ammonium, nitrite and protein at rates of 0.247, 0.07 and 0.096 g-N/g-cell/day, respectively, at 22 degreesC. The remediation rates of ammonium nitrogenous wastes decreased by a factor of eight at 35 degreesC, while the specific growth rates slightly increased. For nitrogenous wastes, ammonium was a preferred substrate but its rate of consumption declined significantly as temperature increased. The nitrogen consumption rates were inconsistent with the cell yields at high temperature. Further analysis of consumption ratios of C/N revealed that cells grew predominantly from the carbon at high temperature. The A. niger NBG5 consumed glucose rapidly at specific rates of 2-2.5 g-C/g-cell/day at 35 degreesC in the presence of ammonium and nitrite; while sluggish consumption of glucose was observed in the protein substrate. The protein could serve as an alternative carbon source. Further ANOVA statistical analysis with P < 0.05 revealed no significant effects of temperature on the specific growth rates of A. niger on the SG-NH4 and milk-protein substrates, whereas significant effects on the ON ratio at culture temperatures higher than 25 degreesC were observed. These findings indicated that the carbon utilization rate increased with high temperature, whereas nitrogen utilization increased as temperature declined. A suitable operational temperature was suggested, depending upon the amount of waste contents of C/N. A high temperature stimulates the use of carbon waste, while a low temperature favors remediation of all nitrogenous wastes. (C) 2003 Elsevier Ltd. All rights reserved.