Water is clearly one of the most important natural resources in the western United States and drought is a major issue in states like New Mexico. Regulation of river flows and land uses in riparian zones and areas linked to them impair aquatic ecosystems and endanger the native biota in regions everywhere. The pervasive effects of humans on aquatic ecosystems reach their greatest magnitude in highly variable ecosystems situated in arid landscapes. The precious value of water, to humans and, in fact, to all life forms on Earth, demands that we look carefully at the changes we inflict on the landscape and seek an understanding of how we might inadvertently be affecting our own future existence. This issue contains articles contributed to a conference on “Aquatic Resources in Arid Lands” that was held in Las Cruces, New Mexico on April 30–May 2, 2003. We organized this conference to bring together prominent aquatic scientists, natural resource agency personnel, and water users to consider issues associated with management of aquatic resources. Invited experts spoke on paleoclimatology, terrestrial-aquatic linkages, ecology, invasive species, decision-support modeling, river restoration, and conservation genetics. The 2-day conference concluded with a half-day facilitated workshop on “Sound Science and Effective Policy for Managing Aquatic Resources.” This issue presents conference research papers on aquatic resources in five categories: climate, hydrology, endangered species, river restoration, and water policy. Climatic uncertainty is the major challenge in managing aquatic ecosystems in arid lands. The first article by Lioubimtseva and Cole addresses the global concern of climate change. Compelling evidence for global warming continues to accrue, although the potential consequence for arid lands is uncertain. Lioubimtseva and Cole argue that the extreme variability of deserts contributes to this uncertainty and they raise the possibility that local and regional human impacts, such as large-scale irrigation projects, may have a greater effect on regional climate than global climate change. In a second article on climate, Hall et al. examine a 40-year climatic record for the upper Rio Grande Basin of New Mexico and Colorado. They report that there is little consistency in time or space in climatic variations across the region. Local regions have climatic shifts in specific periods of the year that appear unrelated to trends in other periods and places. Hydrologic variations in the basin generally indicate trends for elevated river discharge and earlier onset of freshet in recent decades. Understanding hydrologic interactions between surface and groundwaters would enhance water resource management in many ways, especially in regions with most or all of the surface water appropriated for human uses. For the Alcalde Ditch in northern New Mexico, Fernald and Guldan have found that at least 5% of the total ditch flow seeps out