The availability of water resources affects energy, agricultural and environmental systems, which are linked together as well as to climate via the water cycle. As such, watersheds and river basins are directly impacted by local and regional climate variations and change. In turn, these managed systems provide direct inputs to the global economy that serve and promote public health, agricultural and energy production, ecosystem surfaces and infrastructure. We have enhanced the Integrated Global System Model (IGSM) framework capabilities to model effects on the managed water-resource systems of the influence of potential climate change and associated shifts in hydrologic variation and extremes (i.e. non-stationarity in the hydro-climate system), and how we may be able to adapt to these impacts. A key component of this enhancement is the linkage of the Water Resources System (WRS) into the IGSM framework. WRS is a global river basin scale model of water resources management, agricultural (rain-fed and irrigated crops and livestock) and aquatic environmental systems. In particular, WRS will provide the capability within the IGSM framework to explore allocation of water among irrigation, hydropower, urban/industrial, and in-stream uses and investigate how society might adapt water resources due to shifts in hydro-climate variations and extremes. This paper presents the overall design of WRS, its linkages to the land system and economic models of the IGSM, and results of test bed runs of WRS components to address issues of temporal and spatial scales in these linkages.