Abstract In shallow‐water sediments, the combined action of microphytobenthos and bioturbating fauna may differentially affect benthic nutrient fluxes and exert a bottom‐up control of pelagic primary production. In many cases, the effects of microphytobenthos and macrofauna on nutrient cycling were studied separately, ignoring potential synergistic effects. We measured the combined effects of microphytobenthos and chironomid larvae on sediment–water fluxes of gas (O2, TCO2 and N2) and nutrients (NH4+, NO3−, NO2−, and SiO2) in shallow‐water sediments of a hypertrophic freshwater lagoon. Fluxes were measured in the light and in the dark in reconstructed sediments with low (L = 600 ind/m2), high (H = 1,800 ind/m2) and no (C) addition of chironomid larvae, after 3 weeks of pre‐incubation under light/dark regime to allow for microalgal growth. Besides flux measurements, pore water nutrient (NH4+, and SiO2) and dissolved metal concentrations (Fe2+ and Mn2+) were analysed and diffusive fluxes were calculated. Chironomid larvae increased sediment heterotrophy, by augmenting benthic O2 demand and TCO2 and N2 dark production. However, on a daily basis, treatments C and L were net O2 producing and N2 sinks while treatment H was net O2 consuming and N2 producing. All treatments were net C sink regardless of chironomid density. Microphytobenthos always affected benthic nutrient exchange, as significantly higher uptake or lower efflux was measured in the light compared with dark incubations. Theoretical inorganic N, P and Si demand by benthic microalgae largely exceeded both dark effluxes of NH4+, and SiO2 and their net uptake in the light, suggesting the relevance of N‐fixation, water column NO3− and solid‐phase associated P and Si as nutrient sources to benthic algae. Chironomid larvae had a minor effect on inorganic N and P fluxes while they significantly stimulated inorganic Si regeneration. Their bioturbation activity significantly altered pore water chemistry, with a major reduction in nutrient (highest for NH4+ and lowest for SiO2) and metal concentration. Underlying mechanisms are combinations of burrow ventilation and bioirrigation with stimulation of element‐specific processes as coupled nitrification–denitrification, co‐precipitation and inhibition of anaerobic paths such as Fe3+ or Mn4+ reduction or re‐oxidation of their end products. The combined activity of benthic algae and chironomid larvae may significantly attenuate internal nutrient recycling in shallow eutrophic ecosystems, and contribute to the control of pelagic primary production.