Mobility is a fundamental feature of human life, and through it our interactions with the world and people around us generate complex and consequential social phenomena. Social segregation, one such process, is increasingly acknowledged as a product of one's entire lived experience rather than mere residential location. Increasingly granular sources of data on human mobility have evidenced how segregation persists outside the home, in workplaces, cafes, and on the street. Yet there remains only a weak evidential link between the production of social segregation and urban policy. This study addresses this gap through an assessment of the role of the urban transportation systems in shaping social segregation. Using city-scale GPS mobility data and a novel probabilistic mobility framework, we establish social interactions at the scale of transportation infrastructure, by rail and bus service segment, individual roads, and city blocks. The outcomes show how social segregation is more than a single process in space, but varying by time of day, urban design and structure, and service design. These findings reconceptualize segregation as a product of likely encounters during one's daily mobility practice. We then extend these findings through exploratory simulations, highlighting how transportation policy to promote sustainable transport may have potentially unforeseen impacts on segregation. The study underscores that to understand social segregation and achieve positive social change urban policymakers must consider the broadest impacts of their interventions and seek to understand their impact on the daily lived experience of their citizens.