Coastal lagoon sediments are important for the biogeochemical carbon cycle at the land-ocean transition, as they form hotspots for organic carbon burial, as well as potential sites for authigenic carbonate formation. Here, we employ an early diagenetic model to quantify the coupled redox cycling of carbon, iron and sulphur in the sediments of the shallow Ghar El Melh (GEM) lagoon (Tunisia). The model simulated depth profiles show a good correspondence with available pore water data (dissolved inorganic carbon, NH4+, total alkalinity, Ca$^{2+}$, Fe$^{2+}$ and SO$_4^{2-}$) and solid phase data (organic matter, pyrite, calcium carbonate and iron (oxyhydr)oxides). This indicates that the model is able to capture the dominant processes influencing the sedimentary biogeochemical cycling. Our results show that sediment of the GEM lagoon is an efficient reactor for organic matter breakdown (burial efficiency < 10%), with an important role for aerobic respiration (32%) and sulphate reduction (61%). Despite high rates of sulphate reduction, free sulphide does not accumulate in the pore water, due to a large terrestrial input of reactive iron oxides and the efficient sequestration of free sulphide into iron sulphide phases. High pyrite burial (2.2 mmol FeS$_2$ m$^{-2}$ d$^{-1}$) prevents the reoxidation of reduced sulphide, thus resulting in a low total oxygen uptake (4.7 mmol m−2 d−1) of the sediment and a relatively high oxygen penetration depth. The formation of pyrite also generates high amounts of alkalinity in the pore water, which stimulates authigenic carbonate precipitation (2.7 mmol m$^{-2}$ d$^{-1}$) and leads to alkalinity release to the overlying water (3.4 mmol m$^{-2}$ d$^{-1}$). Model simulations with and without an N-cycle reveal a limited influence of nitrification and denitrification on overall organic matter diagenesis. Overall, our study highlights the potential role of coastal lagoons for the global carbon and sulphur cycle, and their possible contribution to shelf alkalinity, which increases the buffering capacity of the coastal ocean for CO$_2$ uptake.