The successful management of groundwater dependent shallow seasonal wetlands requires a sound understanding of groundwater fluxes. However, such fluxes are hard to quantify. Water volume and solute mass balance models can be used in order to derive an estimate of groundwater fluxes within such systems. This approach is particularly attractive, as it can be undertaken using measurable environmental variables, such as; rainfall, evaporation, pond level and salinity. Groundwater fluxes estimated from such an approach are subject to uncertainty in the measured variables as well as in the process representation and in parameters within the model. However, the shallow nature of seasonal wetland ponds means water volume and surface area can change rapidly and non-linearly with depth, requiring an accurate representation of the wetland pond bathymetry. Unfortunately, detailed bathymetry is rarely available and simplifying assumptions regarding the bathymetry have to be made. However, the implications of these assumptions are typically not quantified. We systematically quantify the uncertainty implications for eight different representations of wetland bathymetry for a shallow seasonal wetland pond in South Australia. The predictive uncertainty estimation methods provided in the Model-Independent Parameter Estimation and Uncertainty Analysis software (PEST) are used to quantify the effect of bathymetric uncertainty on the modelled fluxes. We demonstrate that bathymetry can be successfully represented within the model in a simple parametric form using a cubic Be´zier curve, allowing an assessment of bathymetric uncertainty due to measurement error and survey detail on the derived groundwater fluxes compared with the fixed bathymetry models. Findings show that different bathymetry conceptualisations can result in very different mass balance components and hence process conceptualisations, despite equally good fits to observed data, potentially leading to poor management decisions for the wetlands. Model predictive uncertainty increases with the crudity of the bathymetry representation, however, approximations that capture the general shape of the wetland pond such as a power law or Be´zier curve show only a small increase in prediction uncertainty compared to the full dGPS surveyed bathymetry, implying these may be sufficient for most modelling purposes.