We identified the processes governing natural land subsidence in a shallow coastal aquifer near Ravenna (North eastern Italy) by analysing the relationships among different data set time series (water table level, rainfall, drainage, sea level, etc.) and establishing the correlations with vertical ground motion observed at a high-resolution settlement gauge. For the first time we establish the relationships between water table fluctuations and vertical displacement in a real field dataset as well as demonstrate the important contribution of primary consolidation and aquifer stratigraphy to natural land subsidence. Our study highlights the presence of three deformation components related to different processes controlling land subsidence: elastic, delayed-elastic, and irreversible (plastic) components. The elastic and delayed-elastic components are closely related to water table fluctuations that change the effective stress in two portions of the coastal aquifer at a daily (in the sandy unconfined portion) and seasonal time scales (in the finely layered clay-rich semiconfined prodelta portion), respectively. The irreversible component represents the trend in the land subsidence time series and is due to primary consolidation (pore water pressure dissipation) of the fine-grained prodelta levels above where the settlement gauge is located. The amplitudes of the elastic component can be up to 0.2–0.3 mm whereas the amplitude of the delayed-elastic component reaches 0.89 mm. The primary consolidation rate of deformation is 0.9 mm/year and constrains the likely age of prodelta sediments deposition to 1300–2800 years before present. The average degree of consolidation for the prodelta sediments varies from 0.8 to 0.99 according to consolidation coefficients varying from 1.58 to 3.15 m2/year, which are accepted values in the literature. Our analysis point out that primary consolidation in the shallow fine-grained sediments of the shallow coastal aquifer is still ongoing. The delayed-elastic land subsidence rate has similar magnitude to that due to primary consolidation and is likely connected to poroelastic effects in the prodelta sequence following seasonal variations in water table. Our findings are important for planning land subsidence management and monitoring strategies especially where the surface aquifer structure is heterogeneous due to different depositional settings.