In South Florida, approximately 11,000 ha of rice is grown every summer on highly organic histosols. With no added fertilizer inputs of phosphorus (P) or nitrogen (N) as part of the cultivation program, growing flooded rice has the potential to reduce nutrient fluxes from soils to surface water and limit its losses to the water column. Changes in soil redox potential (Eh) will play an important role in the availability of P and nitrate (NO3−) concentration within the groundwater, which ultimately drives the direction of diffusive fluxes across the soil–water interface. The objective of this study was to measure vertical Eh and groundwater concentrations of P and NO3− from commercial flooded rice fields and estimate diffusive fluxes across the soil–water interface. Results indicate that Eh was depth dependent, where deeper soils (30 cm deep) were slightly more anaerobic (mean − 162 mV) than shallow soils (15 cm deep) (mean − 144 mV). Groundwater P concentrations ranged between 0.38 and 1.09 mg L−1 in deep soils (up to 60 cm) and 0.018–0.608 mg L−1 in shallow soils (up to 40 cm). Groundwater NO3− concentrations ranged between 0.065 and 0.64 mg L−1 in deep soils (up to 60 cm) and 0.055–0.499 mg L−1 in shallow soils (up to 40 cm). Diffusive fluxes were mostly positive, which meant they flowed from shallow groundwater to the water column. Phosphorus fluxes were as high as 0.134 mg m−2 d−1 observed in 60-cm deep soils, whereas NO3− fluxes were as high as 0.12 mg m−2 d−1 observed in 40-cm shallow soils. Diffusive fluxes of P and NO3− from flooded rice fields were relatively lower compared to other hydrologic systems.