Multiple fluorochrome experiments with as many fluorochromes as possible are desired for exploring the detailed structure of bioaggregates. Spectral peak interference and other practical limitations, however, restrict the maximum number of stains used simultaneously to three. This current study proposes a sixfold labelled scheme to stain the total cells, dead cells, proteins, lipids, and alpha- and beta-polysaccharides in bioaggregates. Two aerobic granule systems, the phenol-fed and the acetate-fed granules, were utilized as the testing samples for demonstrating the use of the proposed scheme.