High-performance optical detection of toxic heavy metals by using graphene quantum dots (GQDs) requires a strong interaction between the metals and GQDs, which can be reached through a functionalization/immobilization procedure or doping effect. However, commonly used surface activation approaches induce toxicity into the analysis system and, therefore, are ineligible from the environmental point of view. Here, we show that artificial creation of vacancy-type defects in GQDs can be a helpful means of intentional control of the active sites available for reaction with cadmium (Cd), mercury (Hg) and lead (Pb). Using restricted density functional theory (DFT) and time-dependent DFT (TD-DFT) methods, we predict the effect of vacancy complexes not previously studied to describe the binding ability of GQDs towards metal adsorbates. We also show that the interband absorption in closed-shell GQDs complexed with Cd, Hg and Pb is strongly dependent on the vacancy type and can be efficiently tuned to attain the desired coloration of the analysis system. The results suggest that the vacancy defects play an important role in governing the hybridization between locally-excited (LE) and charge-transfer (CT) states of the GQDs. Based on the molecular orbital analysis and in-depth knowledge of excited states, the mechanisms underlying the interband absorption are discussed.