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Plant material used in the construction of segments and beacon towers of the ancient Great Wall in northwestern China contain untapped potential for revealing paleoenvironmental conditions. Here, we characterize the molecular preservation and stable carbon and nitrogen isotope compositions of common reeds (Phragmites) collected from Great Wall fascines dated to the Han Dynasty in today’s Gansu and Xinjiang provinces using a combination of chromatographic techniques and isotope analyses. Our data demonstrates that ancient reeds were harvested from local habitats that were more diverse than exist today. The isotope data also capture differential rates of environmental deterioration along the eastern margin of the Tarim Basin, leading to the intense evaporative stress on modern plants. This study demonstrates the wealth of environmental and climate information obtainable from site-specific organic building material of ancient walls, which have received considerably less attention than the iconic brick and stone masonry walls of the later Ming Dynasty.