Wetland environments are amongst the most dynamic landscapes of Europe. Because of their distinct geomorphological characteristics, they are strongly susceptible for changes in climate, demography, economy and politics. At the same time, these regions reflect areas of long-term human-landscape interactions and outstanding preservation conditions. Large parts of the northern and western Netherlands can be regarded as typical examples of such wetlands. After becoming covered by vast peat marshes over time, these areas were largely reclaimed during the last millennium, which has resulted in a typical landscape consisting of polders and elaborate water-management systems (e.g. canals, dikes, fenlands). This is especially true for the western wetlands, which also are part of the delta of two of the largest European rivers, the Rhine and Meuse. In this area, processes of flooding, fluvial activity and sea-level changes have greatly influenced the landscape, resulting in a very dynamic environment for local inhabitants. Already in the Middle Ages (ad 1050–1500), elaborate organisations and hydraulic systems were set up in these parts in order to ensure water safety and promote water drainage. Through time, these organisations, the so-called waterboards, have greatly influenced the spatial layout of these wetlands and, in doing so, collected huge amounts of data on water management. For the first time, recent digital developments in geosciences and humanities allow us to diachronically unravel the complex interplay between natural and cultural dynamics in such wetlands. In this paper, we present a Historical Geographical Information System (HGIS) designed for modelling heritage in wetland areas. The HGIS specifically focuses on water-management systems in the wetlands of the western Netherlands. We show that (1) our HGIS and GIScience-methodology facilitates an integrated and multi-proxy approach towards studying historical water-management systems, and (2) the developed system is highly suited for unravelling the complex interplay and interdependencies between drainage systems, waterboards and engineering works. Additionally, it becomes clear that by combining information on the past with the present, the HGIS is an extremely useful tool for modern-day policymaking facing future challenges.