The present invention provides a novel nanoparticle drug delivery system generated from poly(ortho ester) polymers with sustained drug release capability and can be functionalized to allow for systemic delivery to various organ systems throughout the body. One important aspect of this invention is that the nanoparticle drug delivery system generated from poly(ortho ester) polymers encapsulate several types of drugs in poly(ortho ester) nanoparticles, including but not limited to lipophilic, hydrophilic small and large molecules and also hydrophilic and lipophilic dyes by adopting appropriate emulsion techniques. These poly(ortho ester) nanoparticles are biodegradable, biocompatible and controlled release drug delivery system with zero order kinetics, which can be used in various biomedical applications such as eye-related diseases, cancer, arthritis, etc.