The effect of climate change on food and water sustainability is an alarming issue worldwide. Food remains found in ancient settlements and mortuary contexts as is the case in ancient Egypt not only embody a list of plant taxa that shaped the people’s diet and cultural foodways but also encode the social and climatic history of Egypt and the Nile River, which is relevant to current issues relating to the anthropogenic impact of climate change and the impact of the damming of rivers on social structure and food and water supply. Food is more than a biological need that sustains our body; it is an active agent in the creation of social structure, economy, personal identity, and cross-cultural relationships. Contextualized analysis of food remains from the archaeological record has served as a powerful lens for archaeologists, anthropologists, and social historians to understand social relations, cultural interactions, and the engendered experiences of individuals in the past. The archaeological record from ancient Egypt has yielded an exceptionally rich array of organic food remains. Indeed, it was the study of botanical materials from Egypt that spearheaded the field of archaeobotany and allowed Willard Libby to invent carbon dating, using seeds from Djeser’s pyramid housed in the Field Museum of Natural History in Chicago, eventually winning him the Nobel Prize for his contribution in archaeology, geology and other branches of science. In this dissertation, I continue this interdisciplinary cross-link between life sciences and the humanities by proposing interdisciplinary analyses to study ancient foodways, and ultimately demonstrate the various ways in which ancient botanical remains can expand our knowledge of ancient Egyptian society in terms of social structure, temporal and regional cultural variation, cross-regional interactions, and cultural relationships, especially in non-elite contexts. The interpretations of the results are carried out within the theoretical frameworks of postcolonial and indigenous archaeologies to transcend, and push the field of Egyptology beyond colonial and oriental origins. Scientific analysis including stable isotope biogeochemistry and ecology applications on well-dated plant-food remains from the archaeological record serve as a scientific tool to record changes in climate, soil fertility, water cycle, and environmental conditions and how they are influenced by different water and agricultural management systems, providing invaluable deep-time data on the anthropogenic impact of climate change on social structure and foodways. First, I present the analysis of unpublished and reanalyzed botanical remains excavated by Reisner and Lythgoe in the early 1900s at the sites of Nag ed-Deir and Deir el-Ballas that are now housed at the Phoebe Hearst Museum at the University of California, Berkeley. This study presents the results of archaeobotanical and molecular isotopic analyses on plant remains from these sites. A nano-archaeological method was also developed as a non-destructive way to identify the ingredients of a beer mash, which was found to have rich fiber content in addition to residue of wild fruits, used as a natural sweetener. This finding is a region-specific recipe, which demonstrates that there was regional cultural variation in ancient Egyptian cuisine, and a difference in nutritional values of food between the past and present foodways in the Egyptian society. This research also presents the result of a long stable isotope experiment, building a baseline for the Nile River, and introduces a new isotopic method using non-exchangeable oxygen isotopes in fruits to identify the source region of plant-food remains, and the environmental and water conditions in which they grew. Such an approach enables us to reconstruct the elements of a social history of food, regional identities, and cross-cultural interactions, ultimately challenging the simplistic assumption that the ancient Egyptian diet was homogenous and predominantly composed of “bread and beer made of wheat and barley”. This is also the first stable isotopic study on archaeobotanical remains from Egypt corroborated with AMS carbon dating. This new combination of methods opens a new direction of research into the history of cultural interactions, providing critical implications for historians, bioarchaeologists, hydrologists, and climate change scientists. This research demonstrates that the analysis of plant food remains through interdisciplinary theories and methods not only contributes to social sciences but is also significant in capturing the environmental history of climatic changes in the past and of important relevance to life sciences as well. Contextualized comparison of these changes by contrasting ancient and modern plant species biodiversity and their isotopic composition can be a significant contribution to the next generation of scientists interested in reversing the impact of climate change on social structure and food and water sustainability.