Climate change and various changes in the landscape itself, such as permafrost thaw, may trigger and mediate substantial changes in the inland water system of the Arctic. Many climate change responses in the Arctic landscape and ecosystems are then related to alterations in the hydrological system. The nature of all these change interactions is not well understood. This thesis aims to improve our understanding of changes in the Arctic inland water system and their interactions with permafrost and ecosystem changes. Investigation of the spatial coverage of systematic hydrological monitoring data and observation data for hydro-climatically related ecosystem shifts, such as large-scale lake-area change, shows that this overlap is small. Yet some monitoring hotspot areas exist, where such data overlap and can be used to improve our understanding of linked hydrological, permafrost and ecosystem changes in the Arctic under climate change. Analysis of lake-change patterns in such hotspot areas indicates permafrost thaw as a main change driver/mediator of some change patterns. However, clear indication of basin-wide influence of permafrost thaw on hydrological discharge dynamics was only found in two relatively small out of total six investigated permafrost basins of different scales. Further, both permafrost and non-permafrost basins exhibit large-scale lake-area changes. A salient change pattern emerging across all investigated basins is an opposite direction of runoff change to that of precipitation change. This contrast is explainable by apparent evapotranspiration changes that may be due to observed changes in surface water (lake) area and associated water-storage changes. Patches of local lake-area change can thus add up to considerable large-scale effects on evapotranspiration and runoff changes. Overall, this thesis shows that linking water system change to permafrost and ecosystem changes is essential for advancing our understanding of Arctic environmental change.