Water plays a key role in the functioning of wetlands and a shortage or contamination of it leads to changes in habitat conditions and degradation of ecosystems. This article scrutinizes the impact of climate change on the hydrological characteristics of floods (maximum flow, duration, volume) in the River Biebrza wetlands (North-East Poland). We analysed the trends in duration and volume of flood and maximum discharges in the historical period 1970–2000 and predicted these for the future periods 2020–2050 and 2070–2100, respectively. Next we assessed the impact on the wetland ecosystems. The basis of our assessments consists of statistical analyses of hydrographs and calculations by the Soil and Water Assessment Tool hydrological model and considering nine bias-corrected climate models. The results indicate that both volume and duration of winter floods will keep increasing continuously under Representative Concentration Pathways 4.5 and 8.5. The reduction in peak annual floods is expected to decline slightly in both scenarios. On the other hand, the analysis of trends in mean and standard deviation revealed negligible tendencies in the datasets for summer and winter hydrological seasons within the three time frames analysed (1970–2000; 2020–2050; 2070–2100). We foresee several future implications for the floodplain ecosystems. Shifts in transversal ecosystem zonation parallel to the river will likely take place with more highly productive flood tolerant vegetation types. Nutrient availability and algal blooms during spring inundations will likely increase. Slowdown of organic matter turnover later in summer will lead to a higher peat accumulation rate. Logistical problems with summer mowing and removal of bushes in winter may enhance shrub encroachment.