The overarching objective of this dissertation was to develop and apply computationally efficient techniques for integrated surface water (SW) and groundwater (GW) modeling to address various changes of hydrologic components under future climate projections. The dissertation research contains two main studies, one focusing on inland lakes in the Northern Highland Lakes District (NHLD) (Chapters 2, 3, and 4), and the other on wetlands in the Kankakee River Watershed (KRW) (Chapter 5). Both studies address the responses of these inland waterbodies to changes in projected future climate over the Midwest for the late 21st century. Relating to inland lakes, Chapter 2 first describes the methodology for the development of an integrated SW/GW modeling framework that is used to generate inputs for a spatially explicit, hydrology-driven lake water budget model, simulating thousands of individual lakes across the NHLD. We demonstrate with these tools that a simplified approach to spatially explicit modeling can produce results comparable with those of more sophisticated and highly calibrated modeling approaches. Chapter 3 then investigates the response of the NHLD under scenarios of future climate change and highlights the variability not only in the projected future climate, but also in the responses across different lake types. The hydrology results from Chapter 3 are then used in Chapter 4 in order to investigate the biogeochemical implications that the changes in lake hydrology may have on lake carbon processing and primary productivity. Chapter 5 introduces a new regional and local-scale GW model designed to simulate the response of riparian and upland wetlands under the same climate projections investigated in Chapters 3 and 4. We found wetlands in the KRW to be robust under all projected future climate scenarios analyzed, with increases in annual average flooding observed across both wetland types at both regional and local scales.