From 2008 to 2014, the MAREL-Iroise buoy, located in the Bay of Brest, collected high-frequency measurements of partial pressure of CO2 (pCO2) and ancillary hydrographic parameters, in conjunction with a comprehensive sampling regime of two additional carbonate system variables total alkalinity (AT), and dissolved inorganic carbon (DIC). Biological processes drive variations in AT and DIC throughout the year, except in winter, when primary production is negligible and large freshwater inputs occur. Annually, the Bay of Brest generally behaves as a source of CO2 to the atmosphere (0.14 ± 0.20 mol C m− 2 yr− 1), showing inter-annual variability significantly linked to annual net community production (NCP). The presence of a large community of benthic filter feeders leads to high levels of particulate organic matter (POM) and opal deposition during the spring diatom bloom. Over the following few months, benthic POM remineralisation reduces the spring CO2 deficit relative to the atmosphere, and remineralisation of biogenic silica supplies further late spring primary production. The result is an inverse spring NCP – air-sea CO2 flux relationship, whereby greater NCP in early spring results in lower fluxes of CO2 into the Bay in late spring. This recycling mechanism, or silicic acid pump, also links the spring and summer NCP values, which are both determined by the peak wintertime nutrient concentrations. The carbonate system is further affected by the benthic community in winter, when CaCO3 dissolution is evident from notable deviations in the ΔAT:ΔDIC ratio. This study highlights the necessity of individual study of coastal, temperate ecosystems and contributes to a better understanding of what determines coastal areas as sinks or sources of CO2 to the atmosphere.