Climatically the Silurian was a most unstable period, as it is shows several strong δ13C excursions, with the Lau excursion being the strongest short-lived positive δ13C excursion of the entire Phanerozoic. The causes of these excursions remain a topic of debate. In order to determine how benthic communities responded to these climatic perturbations, a microfacies analysis of carbonate rocks from the Silurian period (Late Telychian to the uppermost Ludfordian) of Gotland was conducted. The development of reefs was significantly enhanced during periods characterized by carbon isotope excursions, compared to time intervals without. In periods of elevated δ13C values (≥ 3 ‰) the abundance of bryozoans and microbes increases, and in some areas, they form reefs (bryostromatolites), while corals and stromatoporoids were the main reef builders in periods of lower isotope ratios (0–3 ‰). Furthermore, a significant increase of phosphatic components, gypsum pseudomorphs and the microproblematicum Palaeomicrocodium is observed in times of increased isotope ratios. A model is proposed that explains the changes in the benthic communities over time. It is based on previously published models and explains the geochemical processes from coastal areas to the open ocean. Changes are assumed from a humid climate in times without isotope excursions to an arid climate in times of isotope excursions. It emphasizes processes that may have led to the strong δ13C shifts during the Silurian period, and includes the phosphorus cycle in sea water as an important factor in the development of the benthic communities.