As persistent wetlands in arid regions, ciénegas represent important resources for the maintenance and preservation of regional biodiversity. The history of ciénegas in the American Southwest over the last 8,000 years provides information on the dynamics of growth, longevity, and stability of these habitats under previous climate conditions. Proxy data such as sedimentology, pollen, charcoal, and isotopes preserved in ciénega sediments provide information on the formation, disturbance, resilience and state changes within these systems. This long-term perspective is compared to the recent history of degradation observed in the region. Once formed, ciénega surfaces alternate between wetland and dryland phases, identified by changes in pollen preservation and isotopic signatures. These phase changes are hypothesized to be controlled by groundwater-table depths. The degraded state of many extant ciénegas may be similar to the dryland phase, but may also require active management to initiate the natural hysteresis of wetland and dryland phases. We present a conceptual model on the controls for different ciénega states and how the paleoenvironmental record of change can be used in conservation, restoration, and management of these critical habitats.