Riverine dissolved silicon (DSi) and biogenic silica (BSi) are modulated along the estuarine gradient by several biotic and abiotic processes governed by physical forcings. An important area controlling silicon transport in alluvial estuaries with large intertidal mudflats is the benthic diatom-dominated biofilm system. Here, the hypertidal Severn Estuary, UK, has been used as a case study to improve our understanding of silicon transport in these benthic-dominated systems. We present the first time-series dataset of Si concentrations in the Severn. River and tidal hydrodynamics drove spatio-temporal changes in DSi. The longitudinal profile of DSi followed the classical view of dilution with downstream transport. Despite low riverine supply of BSi and low siliceous-phytoplankton production, relatively high BSi concentrations were measured in the Severn Estuary (maximum of 14.9 mg/L), which accounted for over 70% of the total bioavailable silicon present and were characterised by isotopically heavy waters (δ30Si of + 0.9 to + 1.1‰). Benthic biofilms (microphytobenthos) on the intertidal mudflats contained significant biomass (measured as chlorophyll a concentration with a maximum of 116.8 ± 16.2 µg/g dw. sed) with high productivity, driven by their photoprotective adaptions to these harsh intertidal environments, contributing to isotopically heavy mudflat water (δ30Si of + 1.19 to + 2.03‰), and resulting in high benthic BSi content in the spring (0.74 ± 0.03%) and summer (0.76 ± 0.05%). The fast-flowing tidal currents resulted in high bottom shear stress which likely exceeded the erosion thresholds of the biofilms, transporting the sediment-BSi matrix into the water column. Suspended particulate matter (SPM) and BSi remained tightly coupled in the estuarine water column (bioflocculation), and experienced the series of erosion–deposition events, burial/dissolution and export out of the estuary. Our novel observations improve understanding of the complex processes governing Si transport in hypertidal, benthic-dominated estuaries, and highlights the importance of tightly coupled benthic-pelagic systems in influencing the terrestrial silicon export to a marine zone.