BACKGROUND: In this study a comparison between two continuously operating fixed-bed column systems was performed in order to select the best operating conditions in terms of organic sources for sulphate reducing bacteria (SRB). The first column system (solid substrate, SS) was filled with a solid reactive mixture containing the organic matter necessary for SRB growth, while the second one (liquid substrate, LS) was filled with inert material and continuously fed by ethanol. RESULTS: In the SS column 50 +/- 10% sulphate abatement was reached at steady state, while metals were totally removed. Blank tests showed that biosorption was mainly responsible for both sulphate and metal removal. In the LS column, sulphate abatement was 70 +/- 10% at steady state against 10 +/- 5% of an identical column without inoculum (blank liquid substrate, BLS). Comparison with BLS showed that the main mechanism operating in this system was bioprecipitation. Estimated degradation rate constants for both SS and LS columns indicate similar performances (0.008 +/- 0.001 and 0.0085 +/- 0.0005 d(-1) for SS and LS, respectively). CONCLUSIONS: LS column systems offer a valid alternative to conventional SS systems, avoiding the use of potentially harmful wastes as organic sources for SRB metabolism. (C) 2009 Society of Chemical Industry