•Disconnected state-civil society knowledge flows and disconnected socio-ecological systems inhibit efforts to build socio-hydrological resilience to water risks.•Cape Town’s marginalized urban spaces, while physically located at the periphery, are in fact central to the city’s urban social-hydrological systems.•Ignoring marginalized urban spaces does not only disproportionally affect Cape Town’s impoverished communities, but also effectively undermines the socio-hydrological resilience of Cape Town as a whole. In 2017 and 2018, Cape Town faced historically unprecedented water shortages. With the imminent possibility of running out of water, the city’s leadership prioritized reducing water demand and expanding new water sources, while also reinvigorating the goal of seeking to build system-level water resilience for the longer term. Beyond the context of Cape Town, the crisis captured global attention, highlighting ongoing and future water security challenges, the realities of climate change, and the critical need to foster transitions towards more resilient water futures. Given that much of the discourse and implementation around water resilience remains squarely focused on the biophysical and engineering aspects of water supply and distribution systems, despite repeated calls for the need for greater attention to issues of equity and power, there remains little understanding of the ways that persistent inequities might serve or inhibit possibilities for urban socio-hydrological (or water) resilience. This paper draws on examples from Cape Town to argue that patterns and legacies of inequality, marginalization, and exclusion erode and inhibit possibilities for water resilience. Providing needed empirical evidence on the nature of these linkages, we theorize that deeply rooted inequities and related dynamics act as “counter-currents”—trends that undermine and present persistent challenges to efforts to enhance socio-hydrological resilience. Documenting examples of disconnections between the state and civil society as well as disconnected socio-ecological systems, we argue that these persistent inequities mean that efforts to achieve socio-hydrological resilience are likely to remain elusive. It is only by foregrounding these processes that it will be possible to make cities more resilient in the face of ongoing and future water-related risks, uncertainties, and climatic and environmental change.