Climate change is expected to affect the water cycle through changes in precipitation, river streamflow, and soil moisture dynamics, and therefore, present a threat to groundwater and surface water-fed wetland habitats and their biodiversity. This article examines the past trends and future impacts of climate change on riparian, water-dependent habitats within the special areas of conservation (SAC) of the Natura 2000 network located within Odra and Vistula River basins in Poland. Hydrological modelling using the Soil and Water Assessment Tool (SWAT) was driven by a set of nine EURO-CORDEX regional climate models under two greenhouse gas concentration trajectories. Changes in the duration of flooding and inundation events were used to assess climate change’s impact on surface water-fed wetland habitats. The groundwater-fed wetlands were evaluated on the basis of changes in soil water content. Information about the current conservation status, threats, and pressures that affect the habitats suggest that the wetlands might dry out. Increased precipitation projected for the future causing increased water supply to both surface water and groundwater-fed wetlands would lead to beneficial outcomes for habitats with good, average, or reduced conservation status. However, habitats with an excellent conservation status that are already in optimum condition could be negatively affected by climate change as increased soil water or duration of overbank flow would exceed their tolerance.