Coastal areas are subjected to several anthropogenic stressors with much of the world's intertidal areas receding due to human activities, coastal erosion and sea level rise. The Dutch Eastern Scheldt (ES) has been predicted to lose around 35% of intertidal areas by 2060. This study investigates differences between biogeochemical fluxes of intertidal and subtidal sediments of the ES and assesses how ongoing erosion may modify the sedimentary ecosystem functioning of this coastal bay in the coming decades. Monthly fluxes and porewater concentrations of dissolved inorganicnitrogen (DIN), phosphorous (DIP), silica (DSi), carbon (DIC) and oxygen (O ₂) as well as organic matter (OM) characteristics were measured from intertidal and subtidal sediments from June 2016–December 2017. Compared to subtidal stations, OM was significantly more reactive in intertidal samples and exhibited 37% higher O₂ fluxes, suggesting a strong influence from microphytobenthos. Subtidal sedimentsexhibited an average efflux of nitrates (0.28 mmol m⁻² d ⁻¹) and phosphates (0.09 mmol m⁻² d⁻¹) into the water column, while intertidal areas displayed average influxes (nitrates = −1.2 mmol m⁻² d⁻¹, phosphates = −0.03 mmol m⁻² d⁻¹) directed into the sediment. The calculated removal of total DIN and DIP from the water column was 34–38% higher in intertidal compared to subtidal samples suggesting stronger denitrification and phosphorus adsorption to solid particles from intertidal sediments. As an upscaling exercise, we estimate potential erosion induced changes if the ES stations are representative for the system. With this assumption, we estimate 11% and 8% reductions for respective nitrogen and phosphorus removal in the entire ES by 2060. Given the global observations of eroding intertidal areas and rising sea levels, we suggest that the predicted habitat loss may cause significant changes for coastal biogeochemistry and should be investigated further to understand its potential consequences.