Pseudomonas stutzeri was exposed to quantum dots (QDs) with three different surface coatings (anionic polymaleic anhydride-alt-1-octadecene (PMAO), cationic polyethylenimine (PEI), and carboxyl QDs) under both aerobic and anaerobic (denitrifying) conditions. Under aerobic conditions, toxicity (assessed per growth inhibition) increased from PMAO to carboxyl to PEI QDs. The positive charge of PEI facilitated direct contact with negatively charged bacteria, which was verified by TEM analysis. Both PMAO and PEI QDs hindered energy transduction (indicated by a decrease in cell membrane potential), and this effect was most pronounced with PEI QDs under denitrifying conditions. Up-regulation of denitrification genes (i.e., nitrate reductase narG, periplasmic nitrate reductase napB, nitrite reductase nirH, and NO reductase norB) occurred upon exposure to subinhibitory PEI QD concentrations (1 nM). Accordingly, denitrification activity (assessed per respiratory nitrate consumption in the presence of ammonia) increased during sublethal PEI QD exposure. However, cell viability (including denitrification) was hindered at 10 nM or higher PEI QD concentrations. Efflux pump genes czcB and czcC were induced by PEI QDs under denitrifying conditions, even though Cd and Se dissolution from QDs did not reach toxic levels (exposure was at pH 7 to minimize hydrolysis of QD coatings and the associated release of metal constituents). Up-regulation of the superoxide dismutase (stress) gene sodB occurred only under aerobic conditions, likely due to intracellular production of reactive oxygen species (ROS). The absence of ROS under denitrifying conditions suggests that the antibacterial activity of QDs was not due to ROS production alone. Overall, this work forewarns about unintended potential impacts to denitrification as a result of disposal and incidental releases of QDs, especially those with positively charged coatings (e.g., PEI QDs).