Chitosan nanoparticles (CNPs) are known to have great utility in many fields (pharmaceutical, agricultural, food industry, wastewater treatment, etc.). In this study we aimed to synthesize sub-100 nm CNPs as a precursor of new biopolymer-based virus surrogates for water applications. We present a simple yet efficient synthesis procedure for obtaining high yield, monodisperse CNPs with size 68–77 nm. The CNPs were synthesized by ionic gelation using low molecular weight chitosan (deacetylation 75–85%) and tripolyphosphate as crosslinker, under rigorous homogenization to decrease size and increase uniformity, and purified by passing through 0.1 μm polyethersulfone syringe filters. The CNPs were characterized using dynamic light scattering, tunable resistive pulse sensing, and scanning electron microscopy. We demonstrate reproducibility of this method at two separate facilities. The effects of pH, ionic strength and three different purification methods on the size and polydispersity of CNP formation were examined. Larger CNPs (95–219) were produced under ionic strength and pH controls, and when purified using ultracentrifugation or size exclusion chromatography. Smaller CNPs (68–77 nm) were formulated using homogenization and filtration, and could readily interact with negatively charge proteins and DNA, making them an ideal precursor for the development of DNA-labelled, protein-coated virus surrogates for environmental water applications.