The water, food and energy security of millions of people is at risk in several regions of the tropical Andes because climate change is altering water storage in high Andean wetlands (bofedales), lakes and glacier ice. These features play a crucial role in delaying water release, particularly in many semiarid regions with pronounced seasonal precipitation, sustaining baseflows and water quality. Changing water availability impacts both high Andean pastoralist systems and other productive systems downstream, including bigger cities in the inter-Andean valleys. Here we outline the hydrological and geomorphological relationships between glaciers, lakes and bofedal wetlands, and the way in which catchment features such as moraines, talus slopes and sandar interact with catchment hydrology in the tropical Andes of Peru. We present a geomorphological map of catchment features in the Cordillera Vilcanota, Southern Peru, and explore how these features can impact hydrogeological processes. We suggest the ways in which well mapped and dated catchment features can provide a damming or groundwater/surface water exchange mechanism for bofedal development and sustenance. We find that glacial lakes will grow modestly as glaciers retreat, but will not provide an equivalent water storage to compensate for the loss of glacier ice. We find that bofedales are well developed within glacial limits, with glacial processes such as erosion and formation of moraines providing the poorly drained conditions suitable for their development. However, we find that the majority of the bofedales are largely hydrologically independent of contemporary glaciers, and could perhaps buffer water supply as glaciers dwindle and disappear. Such analysis enables an improved understanding of the timeframe for the formation of bofedal wetlands and for them to provide their key ecosystem services of water retention and remediation capacity, buffering drought, providing forage for high-Andean livestock herding, carbon storing and sequestration.