A collaborative study was carried out in order to compare the biodegradable dissolved organic carbon (BDOC) analysis using different indigenous mixed bacterial populations as inocula. The variables examined in the study were the laboratories, the water samples (raw, ozonated or finished water), the origin of the inoculum: suspended bacteria from river waters and attached bacteria onto sand taken from drinking water treatment plants. Variances associated with individual components of this study were isolated: the laboratories represented the highest source of variation (56.6–70.7%), while the inoculum origin contribution to the increase of variance is lower (12–26%). As a conclusion, indigenous mixed bacterial populations (suspended or attached bacteria) may be used reliably as standard inocula in BDOC determinations without introducing excessive variability.