As the climate changes, conjunctive use and management of water resources, or integrated water resources management, has become critically important for water resource planners and managers. Climate variability has resulted in irregular precipitation and temperature patterns, and, in turn, extreme storm events causing floods and frequent droughts. Such extreme events have raised stakeholders’ concerns for water availability. Conjunctive uses of multiple water resources are best management practices/ strategies to address this change in water availability. To implement such strategies, an important aspect gaining a better understanding of the hydrological interconnections among atmospheric water, surface water, and groundwater (three waters) as well as their trends or patterns with climate variations. The Earth’s hydrologic cycle is defined as “the pathway of water as it moves in its various phase through the atmosphere, to the Earth, over and through the land, to the ocean, and back to the atmosphere” (National Research Council 1991). Water in this hydrologic cycle (Chow et al. 1988) may be divided into atmospheric water, surface water, and groundwater (subsurface water). Surface water and atmospheric water transfer to each other through water surface evaporation, evapotranspiration by aquatic plants, and precipitation; groundwater and atmospheric water transfer to each other through near-surface evaporation, evapotranspiration through plants, and deep percolation of precipitation. Surface water and groundwater transfer to each other through seepage when they are hydraulically connected or by infiltration when they are hydraulically disconnected. This three-water transfer has been recognized since the latter part of the seventeenth century (Todd and Mays 2005). The three-water interactions mainly occur on the water’s surface, the land’s surface, and in the vadose zone above the groundwater table, as well as in the hyporheic zone between surface water and groundwater. Along with this water transfer, bio-chemical, physical, and kinetic interactions occur between atmospheric water, surface water, and groundwater. The threewater interactions involve multiple disciplines such as meteorology, surface hydrology, subsurface hydrology, geology, agronomy, pedology, and bio-ecology, to name just a few. Significant advances in understanding three-water interactions have been made over the last several decades. For example, advances in interactions between groundwater and surface water have been overviewed (Winter 1995, 1999; Sophocleous 2002; Diiwu 2003) since the growth in research related to surface-subsurface exchange processes mushroomed during the 1990s (Stanley and Jones 2000). Winter (1995) reviewed advances in understanding the interaction of groundwater and surface water in different landscapes: mountain, riverine, coastal, hummocky, and karst terrains. Winter (1999) proposed three general theoretical considerations regarding the interaction of groundwater with surface water. This interaction is affected by (1) different-scale groundwater flow systems, (2) local soil and geologic controls on seepage distribution, and (3) the magnitude of transpiration directly from groundwater around a surface-water perimeter since this transpiration intercepts potential groundwater inflows or draws water from surface-water bodies. Sophocleous (2002) synthesized and exemplified the interactions between groundwater and surface water in relation to climate, landform, geology, and biotic factors. Diiwu (2003) reviewed fundamental concepts of the ecohydrology of the interaction between groundwater and surface water, and discussed the relevance of this interaction to the sustainable management of water resources in semi-arid regions. A task committee (see subsequent information) was established within the Groundwater Council to promote scientific exchange and share experiences by inviting scientists and researchers to prepare articles and presentations focusing on the state of science relative to the interaction of atmospheric water, surface water, and groundwater, and on the impacts of climate change on water resources, as well as their conjunctive management and uses. This special section includes a collection of invited and peer-reviewed papers including field investigations, numerical simulations, and practical case studies on the following topics: physical/hydrological characterization of interactions; analytical and numerical models for simulating interactions; conjunctive uses and management of the three waters; climate change impacts on interaction of the three waters, including extreme events such as floods and drought; and water quality issues related to such interactions. In this special section, authors present their recent research findings on the interactions of the three waters and their associated processes. It is anticipated that this collection will promote further scientific exchange and further advances of our knowledge in this research area. We are very appreciative of the authors’ contribution and efforts and of the constructive comments and timely reports by reviewers and editors.