Some embodiments provide methods for calibrating a fluorometer in order to account for one or more optical properties of a water sample affecting fluorescence measurements. In some cases one or more calibration solutions are prepared with sample water from a specific field site. Fluorescence measurements are taken from a water sample and one or more of the calibration solutions, and calibration parameters are determined based on the measurements. In some cases a calibration solution is prepared by spiking sample water to include a higher concentration of a fluorescent tracer and measurements are taken to characterize a calibration slope coefficient. In some cases a calibration solution is prepared by adding an acid and measurements are taken to characterize a background fluorescence in the sample.