Porewater fluxes, including fresh groundwater discharge and circulation of surface waters through sediments, are increasingly documented to play an important role in hydrological and biogeochemical cycles of coastal water bodies. In most studies, the magnitude of porewater fluxes is inferred from geochemical tracers, but a detailed understanding of the underlying physical forces driving these fluxes remains limited. In this study, we evaluate the mechanisms driving porewater fluxes in the shallow coastal La Palme lagoon (France). We combined measurements of variations of salinity and temperature in the subsurface with 1-dimensional fluid, salt and heat transport models to evaluate the dynamics of porewater fluxes across the sediment-water interface in response to temporally variable forcings. Two main processes were identified as major drivers of porewater fluxes: i) temporal variations of lagoon water depths (forcing porewater fluxes up to 25 cm d−1) and ii) locally-generated wind waves (porewater fluxes of ~50 cm d−1). These processes operate over different spatial and temporal scales; Wind-driven waves force the shallow circulation of surface lagoon waters through sediments (mostly < 0.2 m), but are restricted to strong wind events (typically lasting for 1–3 days). In contrast, porewater fluxes driven by variations of lagoon water depths flush a much greater depth of sediment (>1 m). The spatial and temporal scales of driving forces will largely determine the significance of porewater fluxes, as well as their chemical composition. Thus, an appropriate evaluation of the magnitude of porewater-driven solute fluxes and their consequences for coastal ecosystems requires a solid and site-specific understanding of the underlying physical forces.