The present research was conducted to study the column mode (down flow and up flow) of Aspergillus niger decomposed Citrus limetta peels powder for desalinating Cd2+ and Pb2+ from synthetic and paint industrial wastewater. The batch mode was carried out to optimize pH, contact time, initial metal ion concentration and adsorbent doses. The column studies (both down flow and up flow) were performed with paint manufacturing industrial wastewater at optimized conditions. The percentage removal, metal uptake capacity and exhaustion time of the column in up flow mode were found to be far better as compared to down flow mode. The value of metal uptake capacity for Cd2+ and Pb2+ was achieved to be 722 and 596 mg g−1 at pH 5.0 and 6.0, respectively, in the first cycle using Thomas model. The comparison of adsorption in single- and multi-metal ion systems showed that A. niger decomposed C. limetta peels powder have an excellent potential for the removal metal ions from industrial effluents.