Abstract: Given sufficiently strong internal feedbacks, ecosystems may exhibit multiple stable equilibria under a given set of conditions. Transitions between alternative states (i.e., regime shifts) can occur in response to changing conditions or disturbance, and subsequent return to the original equilibria can be resisted by re-organization of internal feedbacks (i.e., hysteresis). In desert streams, sudden and widespread erosion of historically-abundant wetlands (ciénegas) during the late 19th and early 20th centuries resulted in incised channels transporting coarse sediment loads and supporting little vegetation. More recently, the re-establishment of ciénega patches in Sycamore Creek, AZ, site of long-term research on desert stream ecosystems, provides an opportunity to understand the causes and consequences of wetland formation and persistence in these severely hydrologically disturbed ecosystems. In the absence of vegetation, biogeochemical processes in desert streams are driven by flash flood disturbance and subsequent recovery and by hydrologic and material exchange between surface and subsurface (hyporheic) flowpaths. In contrast, subsurface waters of wetland patches are consistently anoxic and unresponsive to small-to-moderate-sized floods, during which they accumulated fine sediments and organic matter. Thus the establishment of vegetation reduces the importance of post-disturbance succession and surface-subsurface exchange as determinants of biogeochemical processes. However, field surveys and greenhouse microcosm experiments indicate that, like algae in the gravelbed system, herbaceous plants in desert streams are limited by the availability of nitrogen (N). Increases in plant growth associated with N enrichment alleviated carbon (C) limitation of heterotrophic hyporheic microbes and promoted increased denitrification and N retention efficiency. In a simple model of vegetation response to floods, sediment stabilization by vegetation generated alternative-stable-state behavior. In support of this hypothesis, a two-year field survey of vegetation demonstrated negative relationships between density of vegetation and per-capita losses and divergence of vegetation abundances towards a bimodal distribution in response to flood events. Identification of ciénegas as alternative stable states supports the recently-proposed hypothesis that systems with severe abiotic disturbance regimes are more likely to exhibit alternative stable states. This model further suggests that climate regime and local geomorphic structure interact to influence the resilience of cienegas and other biogeomorphic systems.