The present study examines the effect of carboxyl-CdSe/ZnS quantum dots (QDs) on Cu and Pb availability to microalgae with different cell wall characteristics: Chlorella kesslerii possessing a cellulosic cell wall and two strains of Chlamydomonas reinhardtii, a wall-less and a walled strain containing glycoproteins as the main cell wall component. Results demonstrated that QDs decreased Pb and Cu intracellular contents ({Cu}int and {Pb}int) inwalled strains by a factor of 2.5 and 2, respectively, as expected by the decrease of about 70% and 40% in the dissolved Cu and Pb concentrations. QDs increased {Cu}int and {Pb}int in wall-less strain by a factor of 4 and 3.5. These observations were consistent with the observed association of QDs to the wall-less C. reinhardtii, and lack of association to walled algal strains. Suwannee River humic acid did not influence metal association to QDs, but decreased {Cu}int and {Pb}int in all microalgae.