Quantum dot (QD) aggregate formation is essential, especially, in nanoparticle-based drug delivery systems. Imaging of these targeted QD aggregates exposes information about the the treatment of many diseases including cancer. Scanning Acoustic Microscopy (SAM) is a non-invasive and rapid imaging modality, which can obtain qualitative and quantitative features simultaneously. In our study, acoustic impedance microscopy of QD aggregates was performed by SAM for evaluating the potential of SAM in the detection of lead-sulphide (PbS), graphene and cadmium-telluride/cadmium sulphide (CdTe/CdS) quantum dot aggregates for the first time. Absorption spectra of QDs, obtained with an ultraviolet-visible spectrometer, and fluorescence spectra of QD aggregates, obtained with an inverted fluorescence microscope, are also demonstrated. The success of imaging quantum dot aggregates by SAM indicated the potential of SAM in monitoring the micro-environment of the disease and also the therapeutic effect of the drug-loaded QD aggregates.