This invention relates generally to a system and process for early detection of biological ammonia oxidation in water utilizing a fluorescence-based sensor and process. Various embodiments are configured to read increases in a fluorescence excitation-emission wavelength pair that is responsive to a period of time (days to weeks or even longer) prior to the onset of biological ammonia oxidation, which is considered to be a nitrification event. Fluorescence excitation/emission pairs that have proven to be reliable include a fluorescence excitation wavelength of about 230 nm and an emission wavelength of about 345 nm and an excitation wavelength of 325 and an emission wavelength of 470. The system and process enable drinking water utilities to improve management of its distribution systems and facilitate earlier corrective actions, resulting is less loss of treated water through flushing and other tangible benefits.