Human oral commensal Candida yeasts, as well as environmental free-living amoebae (FLA) such as Hartmannella, are known to be direct or indirect human pathogens. These microorganisms may be isolated from dental unit waterlines (DUWL), because of contamination coming from the tap water and/or a patient's mouth. This study compared the efficacy of commonly used DUWL disinfectants (chlorine, H2 O2 , and Oxygenal 6©) against three species of Candida (C. albicans, C. glabrata, and C. parapsilosis) and one FLA species (H. vermiformis), growing either as single or as mixed biofilms in tap water. Results showed variable efficacies: H2 O2 had no significant activity, while chlorine was effective but only at the highest doses tested, probably not compatible with DUWL uses. Oxygenal 6© was the most efficacious in preventing the growth of yeasts in tap water. However, in the presence of FLA, Oxygenal 6© displayed a reduced antimicrobial activity against sessile C. albicans. In conclusion, none of the tested disinfectants could eradicate yeasts or FLA. Moreover, the antiyeast activity of Oxygenal 6© was reduced in the presence of FLA. Both sessile or planktonic and mixed or single-species conditions should be considered when evaluating the activity of disinfectants for DUWL maintenance. This study also highlighted that FLA should be included in the testing protocols.