Microphytobenthos (MPB) are recognised as exerting an important controlling influence over carbon (C) and nitrogen (N) flows in euphotic sediments, however, the coupling between these flows remains poorly studied. We undertook an inverse model analysis of C and N fluxes through the microbial compartment on intertidal flats in a temperate estuary. The analysis showed that the trophic balance of the sediment exerted a strong influence on the relative fluxes of C and N through the sediment microbial community. Under increasingly autotrophic conditions (P:R > 1), the assimilation of C relative to N rose above the cellular C:N ratio of MPB, resulting in increased excretion rates of organic matter by MPB. The C:N ratio of the organic matter excreted was also highly variable ranging from ~20 (mol:mol) under heterotrophic conditions, and increasing to in excess of 50 under autotrophic conditions. The relative fluxes of C and N through bacteria were also significantly affected by the trophic balance of the sediment and the ratio of C:N mineralized by bacteria was significantly higher under autotrophic conditions. Dissolved organic nitrogen (DON) release by bacteria and uptake by MPB also predominated over inorganic N forms under autotrophic conditions. We conclude that C and N fluxes through shallow euphotic sediments may become significantly decoupled, and well above commonly assumed Redfield ratio and measured cellular C:N ratios of MPB.