The integration of water management goals in protected wetland areas agriculturally managed in an intensive manner recalls the comparison of apples (ecological values) and oranges (economic dimension of agriculture). Sustainable wetland management frequently fails if environmental features are not referred to as ecosystem services and quantified in economic terms. In our hydrological-economical study on floodplain wetlands located in the Lower Basin of the Biebrza Valley, we attempt to quantify the monetary value of water storage in the floodplain during flood phenomena as an important ecosystem service. The unit monetary value of water storage in the catchment of Biebrza Valley was assessed on the basis of small artificial water reservoirs, constructed in recent years and located in the area of research, and reached 0.53 EUR·m−3·year−1. In a GIS-based study on hydrological floodplain processes in the years 1995–2011, we assessed the average annual volume of active water storage in the floodplain which reached 10.36 M m3 year−1, giving a monetary value of EUR 5.49 million per annum. We propose that the methodology presented in our analysis could be applied as water storage subsidies in valuable floodplains, to prevent their deterioration originating from agriculture intensification.