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Seasonal measurements of total and diffusive benthic fluxes were performed during the ice-free period in the Curonian Lagoon (Lithuania). This mostly freshwater hypertrophic basin exhibits wide seasonal variations of water temperature (1-22°C) and inorganic nitrogen availability and it is subjected to dramatic blooms of diatoms and cyanobacteria (>100 μg chl a l-1). In this shallow lagoon, nutrient exchanges at the sediment-water interface and the regulating factors have been poorly explored. Overall aim of the present work is to demonstrate that the activity of benthic microalgae, generally neglected in turbid systems, can be a relevant regulator of sedimentary processes. To this purpose, light and dark fluxes of oxygen, ammonium and soluble reactive phosphorus were measured seasonally by intact core laboratory incubation and diffusive fluxes were calculated from sediment profiles. We investigated sandy sediments that were collected from the central area lagoon, that is representative of the most of the shallower lagoon area.Oxygen and ammonium fluxes were significantly different under light and dark incubations, suggesting an active role of benthic microalgae at the sediment-water interface. In the light net oxygen production was measured in three out of four samplings, with July as only exception, and ammonium was retained within sediments. In the dark sediment respiration displayed a temperature-dependent pattern while ammonium efflux increased from March to October. Fluxes of reactive phosphorus varied significantly with sampling seasons but were less affected by the incubation condition. Diffusive fluxes peaked in July, where highest concentration gradients at the interface and theoretical efflux of ammonium and reactive phosphorous were calculated. The marked differences between diffusive and total nutrient fluxes are probably due to photosynthetic activity by benthic microalgae, and thus oxygen production, enhancement of aerobic processes and net solute uptake at the sediment-water interface. Our findings support the hypothesis that even in highly turbid systems benthic microalgae can have a relevant role as filters for regenerated nutrients and as regulators of benthic processes.