Nanotechnology is the study of materials in the nanoscale. By its nature, nanotechnology is interdisciplinary. Nanotechnology has made a significant stride in recent two decades in various industries. Numerous nanomaterials are devised for biomedical applications which include intracellular tracking and labeling, gene detection and hybridization, tumor or tissue targeting, pharmaceutical therapies, pathogenic inhibiting, and medical instrument coating for disinfections. High photostability and quantum yield of fluorescent nanoparticles are ideal for long-term monitoring of molecular events in living organisms. Here, we discuss delivery of three fluorescent nanoparticles in A549 cells, rotifers, Gram-negative bacteria, Gram-positive bacteria, and archaea. As these nanoparticles cannot enter cells, arginine-rich cell-penetrating peptides (CPPs) were used to enhance their internalization at the cellular or organismal level. The 1-(4,5-dimethylthiazol-2-yl)-3,5-diphenylformazan (MTT) assay and sulforhodamine B (SRB) assay demonstrated that CPP complexed fluorescent nanoparticles did not produce lethal effect in all organisms tested. The discussion of these nanomaterials in this chapter intends to broaden our understanding of their biocompatibility in organisms of various hierarchical levels.