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Subtle bedrock depressions called gnammas allow the water in ephemeral pools to maintain contact with bare rock, thus serving as natural rock‐weathering experiments. Following filling by precipitation, evaporation is often assumed to be the sole process of water loss from gnammas. We evaluated this assumption by monitoring evolving stable isotope compositions of gnamma waters hosted in granite of Colorado's Front Range. Surprisingly, we found that a significant fraction of the water was lost by seepage through the underlying bedrock. Seepage dominated, with only 10%–20% loss by evaporation. We propose a conceptual model of gnamma formation in which enhanced weathering of the bedrock beneath the gnamma increases the water holding capacity and permeability of the underlying rock that in turn promotes efficient water loss through seepage and further weathering of the surrounding rock. This model has implications for bare‐rock weathering and hence the evolution of landscapes over geologic timescales. Plain Language Summary Rates and styles of rock weathering influence the evolution of soil, landforms, and climate over geologic timescales. Gnammas are depressions in solid bedrock that periodically fill with rainwater or snowmelt to form ephemeral pools that can provide critical but temporary water sources in arid, bare‐rock surface environments. In contrast to previous assumptions that gnamma water is lost solely by evaporation, our work shows that a significant fraction of the water can be lost by seepage into the underlying rock. These findings suggest a feedback between enhanced seepage into underlying bedrock and enhanced degradation of the surrounding rock that potentially explains the growth and persistence of these unique isolated ecosystems, and informs debates about the role of bare bedrock weathering in landscape evolution. Key Points Water stable isotopes constrain the hydrologic evolution of gnammas Gnammas lose water via seepage through the underlying bedrock, not only by evaporation Seepage may drive a feedback process that enhances bedrock weathering but limits gnamma size evolution