Floodplain wetlands in arid and tropical environments are intermittently or seasonally flooded, drying for months and up to years in arid wetlands between floods. Aquatic food webs in these systems are adapted to this variable water regime; pulsing in productivity and diversity after floods, yet dependent on nutrients generated during dry cycles. In floodplain wetlands, upstream dams and irrigated agriculture have reduced floods and extended drying, leading to changes to natural levels of productivity and diversity. Environmental flows can contribute to the sustainable management and restoration of degraded wetlands in agricultural landscapes. Decisions on the timing, frequency, duration and magnitude of environmental water allocations depend on sound knowledge of ecological thresholds, and indicators to measure success or failure of management interventions. Thresholds are discussed for concentrations of carbon, ecosystem metabolism and microinvertebrates in arid wetlands as indicators of key ecosystem functions. This approach is also relevant to floodplain wetlands in tropical climates where water managers must balance environmental and agricultural needs in the midst of the uncertainty of climate change.