The present Thesis reports an articulated research work that covers several aspects connected with the modeling of subsurface hydrology of organic soils in connection to the main hazards induced by land subsidence of peatlands and the conservation and wise use of wetlands in the Venetian area. The dynamics of peatland surface deformation both at long and short time scale is studied and a novel two-step modeling approach is proposed to separate the reversible and irreversible components of the land surface displacement. An empirical relationship is calibrated on the estimated irreversible component of the ground displacements recorded in a 4-year long experimental study in a ?eld site located in the Zennare Basin,Italy. The expected evolution of the Venetian peatland over the present century is then investigated. The study of the hydrology of organic soils is then focused on the hysteretical behavior of the moisture retention curve measured in the peat soils of the Zennare Basin. The results of the application of a modeling approach that couples an hysteresis model with a relationship that links the soil matrix porosity dynamic to water saturation bring out the importance of including the swelling/shrinkage phenomenon in the description and prediction of water flow into organic soils. In the last part of the Thesis the focus is shifted to the hydrological dynamics of salt marshes, delicate intertidal zones characterized by a strong hydrological connection between the atmosphere and the subsurface mainly in terms of air fluxes. A two-phase flow model is developed in order to investigate the effects of air flow in the wetlands dynamics. A pressure-based formulation is chosen to allow for natural treatment of the complex and nonlinear boundary conditions to be imposed at the soil-atmosphere interface to take into account the interplay between evapo-transpiration during emersion periods and tidal fluctuations during soil submersion. The results of the application of the model to some test cases aimed at verifying the effect of the inclusion of the air dynamics in the simulation of the water flow in the vadose zone are presented.