Using numerical experiments with a three-dimensional baroclinic hydrodynamic model of the Baltic Sea, which covers the refined grid area around the Neva Delta and Neva Bay, and takes into account the operations of the Saint Petersburg Flood Prevention Facility Complex (FPFC), we investigate the influence of modern alluvial areas on sea level changes in the Neva Bay and Neva Delta during storm surges, under different volumes of Neva River discharge. The hydrological conditions that developed in early December 2015, when Storm Desmond approached St. Petersburg, which caused three dangerous level rises in the east of the Gulf of Finland, one after the other. The alluvial deposits of territories do not have noticeable changes in the sea level of the Neva Bay with the gates of the FPFC closed during storm surges. It is shown that, depending on the runoff of the Neva, with the gates of the FPFC closed, additional sea level rises in the Neva Bay due to alluviation do not exceed 1–5 cm, while in the Neva Delta they reach 20.5 cm. The rise of the sea level to 161 cm at the Mining University, at which floods are recorded in St. Petersburg, occurs due to alluviation 1–2 hours earlier. At the maximum volume of Neva runoff for the autumn-winter period, 27 hours after the closure of the gates of the FPFC, a dangerous flood is recorded in the Neva Bay near the Mining University point, and 48 hours later — a particularly dangerous one.