Volusia Blue Spring (VBS) is the largest spring along the St. Johns River in Florida (USA) and the spring pool is refuge for hundreds of manatees during winter months. However, the water quality of the spring flow has been degraded due to urbanization in the past few decades. A three-dimensional contaminant fate and transport model, utilizing MODFLOW-2000 and MT3DMS, was developed to simulate boron transport in the Upper Florida Aquifer, which sustains the VBS spring discharge. The VBS model relied on information and data related to natural water features, rainfall, land use, water use, treated wastewater discharge, septic tank effluent flows, and fertilizers as inputs to simulate boron transport. The model was calibrated against field-observed water levels, spring discharge, and analysis of boron in water samples. The calibrated VBS model yielded a root-mean-square-error value of 1.8 m for the head and 17.7 μg/L for boron concentrations within the springshed. Model results show that anthropogenic boron from surrounding urbanized areas contributes to the boron found at Volusia Blue Spring.