Climate change is affecting many aspects of the hydrological cycle worldwide. Observed changes include changes in water levels in many wetlands, expansion of thermokarst lakes in the Arctic, changes in the intensity and frequency of precipitation in semi-arid and Mediterranean climates, and changes in water inputs from mist, fog, and dew in tropical mountain forests (in addition to the direct human drainage of tropical peatlands now occurring at an unprecedented rate). These changes will influence ecosystems in complex, non-linear, and conflicting ways. Understanding the impacts of hydrological changes on greenhouse gas emission is particularly challenging, as several key environmental variables such as soil temperature co-vary with soil moisture and phenological changes throughout the year. Large-scale water manipulation experiments present an opportunity to understand current and future impacts of hydrological changes on a variety of ecosystems. Field water manipulations have been conducted for a number of years on ecosystems such as Arctic tundra (Large Scale Water Table Manipulation at Barrow, Alaska), tallgrass pairie (Konza Prairie Biological Station, KS), temperate forest (Throughfall Displacement Experiment in Oak Ridge, TN) and Mediterranean shrubland ecosystems (Puéchabon, France). Networks of ecosystem manipulation experiments have been coordinated for a number of years such as PrecipNet, TERACC, Vulcan, MIND, ClimMani and Carboextreme. There is now an opportunity to synthesize the accumulated information and knowledge to better understand how future changes in the hydrological cycle may affect greenhouse gas emissions from ecosystems worldwide. This special issue will gather contributions studying the impacts of changes in water availability on terrestrial ecosystems, with an emphasis on large-scale manipulation experiment to study the effects on biogeochemical cycles and especially on net greenhouse gas emissions.