Viewing the construction processes of urban spaces through urban political ecology reveals a context that deals with the production of nature as space. Considering the age of ecological rift in which we live, the urgency for understanding and altering the complicated relationship between society and nature, institutionalized mainly through urban design and architectural projects in modern times, is apparent. For doing this, unfolding the urban metabolism of cities will have an essential place in the future. This dissertation explores the concept of urban political ecology as a perspective for understanding the shifting urban metabolism of İstanbul in the period between 1839 and 2019. It aims to develop an approach for understanding socio-natural production and the transformation of the urban space concerning the actions of political events and forces in the context of waterfronts through urban metabolism embedded in particular metabolic flows. First, it traces the particular metabolic flows that constitute the space-making agenda embedded in the political-economic vision, projection, and struggle of each studied sub-period. Second, it records the transition and struggle from a labor-intensive urban metabolism to a capital-intensive urban metabolism in İstanbul between 1839 and 2019. Third, it follows the critical role of architectural practice and urban agenda as political instruments that operate through metabolic flows concerning the shifting urban metabolism of İstanbul within the perspective of urban political ecology. In short, this dissertation makes an original contribution to the context of urban metabolism and the efforts of urban studies at large to transcend the dualities between the social and natural. Moreover, it contributes to discovering the shifting ideology of nature through the space-making agenda and keeping the records of the unfinished urban projections of one period in İstanbul that were completed in another. Above all, this dissertation aims to criticize waterfronts as metabolized socio-natures under the capitalist mode of production. It focuses on the evolution of different types of visions and projections for waterfronts and relationally inner parts of the city throughout the metabolic flows of land, water, urban voids, oil, coal, iron, and cement, respectively. Accordingly, this study seeks to provide critical insights for the next generation of research on the urbanization process in critical architectural and urban studies as well as how this process may affect the socio-natural landscapes of human health and ecosystems.