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1. Feedbacks between vegetation and geomorphic processes can generate alternative stable states and other nonlinear behaviours in ecological systems, but the consequences of these biogeomorphic interactions for other ecosystem processes are poorly understood. In this study, we describe the changes in the hydrological, geomorphic and biogeochemical characteristics of the hyporheic zone of a Sonoran desert stream (Sycamore Creek, Arizona, U.S.A.) in response to a transition from an unvegetated gravel-bed state to densely vegetated wetlands (cienegas).

2. A survey of the entire length of Sycamore Creek indicated that cienegas occupied c. 18% of the stream, and were disproportionately represented in constrained canyons rather than wide, unconstrained valleys.

3. Vegetated patches were characterized by low concentrations of dissolved oxygen (DO) and nitrate and high concentrations of carbon dioxide and methane in the hyporheic zone. In contrast to unvegetated areas, hyporheic DO in cienegas exhibited no relationship with vertical hydraulic gradients.

4. Increases in hyporheic DO following removal of vegetation by floods supports the hypothesis that these reduced conditions were the result of biogeochemical and geomorphic changes associated with vegetation establishment. In locations where vegetation persisted, hyporheic DO exhibited no response to flooding; in sections where vegetation was removed hyporheic DO closely tracked post-flood increases in surface stream DO.

5.Shallow sediments in vegetated patches were finer and more organic-rich than in unvegetated patches, due to increased deposition during floods. Conservative tracer additions indicated that hydrological exchange between the surface stream and hyporheic zone was much lower in cienegas than in gravel-bed reaches.

6. Vegetation establishment in desert streams not only alters the physical and chemical characteristics of the hyporheic zone, but also the nature of interactions between surface and hyporheic subsystems.