Benthic vegetation at the land-water interface is recognized as a filter for silica fluxes, which represents an important but under-investigated subject. This paper aims to analyze stocks and fluxes of biogenic (BSi) and dissolved (DSi) silica in relation to nitrogen (N) and phosphorus (P) in the littoral zone of a deep lake. Specifically, we evaluated how different primary producers can influence BSi retention and DSi release. The study was performed from April to October in 2017, in three different benthic communities: submerged aquatic vegetation (SAV) and microphytobenthos (MPB), both occurring in soft bottom sediments, and epilithic macro- and microalgae (EA) on rocky substrates. The main result was that SAV and MPB were a DSi source and a N and P sink with the DSi efflux from SAV nearly three times as much as in MPB patches. These findings corroborate the hypothesis that SAV mediates the DSi transport from pore water to the water column. Conversely, EA communities were a DSi sink and a N and P source. Overall, these results highlight the fact that the littoral zone of lakes plays a key role in regulating aquatic Si cycling, which is likely to depend on the health status of SAV communities.