Primary production of microphytobenthos (MPB) contributes significantly to the total production in shallow coastal environments. MPB is a diverse community in which diatoms are usually the main microalgal group. Diatoms require N, P, and other nutrients as with other autotrophs, but in addition require silicate to create their outer cell wall. Therefore, dissolved silica (DSi) might be a potential limiting factor for benthic primary production in areas with reduced freshwater input. To test this hypothesis, a microcosm experiment was conducted using intact sediment cores collected from an intertidal mudflat in the Bay of Cádiz and supplied with increasing concentrations of DSi (0, 5, 10, 25, and 45 μmol · L−1). After 7 d of enrichment, we determined chlorophyll a and c (Chl a, c) contents, metabolic rates (Net [Pn] and Areal Gross [PgA] Production and Light [RL] and Dark [RD] Respiration), as well as fluxes of inorganic nutrients across the sediment‐water interface. Chl a and c contents increased significantly with respect to the initial conditions but no differences between treatments were found. Both Pn and PgA showed a saturating‐like pattern with silicate concentration, reaching maximum rates at a DSi concentration of 45 μmol · L−1. The addition of DSi also resulted in an increase of DSi and ammonium uptake by the sediment, which was significantly higher in light than in darkness. Our results clearly show that water column DSi concentrations have a direct impact on benthic primary production, also controlling other related processes such as inorganic nutrient fluxes.