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Abstract The restoration of urban estuaries is challenging due to the complexity of prioritizing sites in a context of social and biophysical unevenness. Site prioritization and selection are crucial components of ecological success and equity in restoration. In many cases, site prioritization is conducted according to simple opportunity or political expediency, but this needs to be investigated further in local contexts, with accompanying analysis of the impacts on urban environmental equity. Using a critical physical geography framework, I explore site selection processes in the restoration of Biscayne Bay through case studies of two urban streams. I use multiple data types to present an integrated perspective on urban restoration priority and the social context that produces restoration siting decisions. I find that the logics of restoration site selection in the Biscayne Bay watershed have produced ecologically questionable decisions and inequitable outcomes. Therefore, I argue that restoration decision making needs to include environmental justice criteria.