Radium isotopes and radon are routinely used as tracers to quantify groundwater and porewater fluxes into coastal and freshwater systems. However, uncertainties associated with the determination of the tracer flux are often poorly addressed and often neglect all the potential errors associated with the conceptualization of the system (i.e., conceptual uncertainties). In this study, we assess the magnitude of some of the key uncertainties related to the determination of the radium and radon inputs supplied by groundwater and porewater fluxes into a waterbody (La Palme Lagoon, France). This uncertainty assessment is addressed through a single model ensemble approach, where a tracer mass balance is run multiple times with variable sets of assumptions and approaches for the key parameters determined through a sensitivity test. In particular, conceptual uncertainties linked to tracer concentration, diffusive fluxes, radon evasion to the atmosphere, and change of tracer inventory over time were considered. The magnitude of porewater fluxes is further constrained using a comparison of independent methods: (1) 224Ra and (2) 222Rn mass balances in overlying waters, (3) a model of 222Rn deficit in sediments, and (4) a fluid-salt numerical transport model. We demonstrate that conceptual uncertainties are commonly a major source of uncertainty on the estimation of groundwater or porewater fluxes and they need to be taken into account when using tracer mass balances. In the absence of a general framework for assessing these uncertainties, this study provides a practical approach to evaluate key uncertainties associated to radon and radium mass balances.