Interactions among social inequalities, environmental stressors, and shocks are illustrated through communities’ subjective experiences of water-related challenges and responses to crises. This situation is perhaps most visible in the COVID-19 pandemic’s impact on marginalized communities where climate change and systemic inequities are already threatening access to water and sanitation. It is critical to integrate dimensions related to well-being into research about vulnerable communities’ capacities and strategies for coping and adapting to such crises. Here, we investigate water-related risks to health and well-being using a subjectivity lens, a particularly useful tool for understanding community-level resilience to lesser-known stressors and crisis impacts. To inform this study, we used households’ self-reported water issues in Cape Town, South Africa’s low-income areas from before the pandemic, in addition to community responses during the pandemic. The findings show how inadequate access to water and sanitation affects people’s health and well-being, both directly by exposure to wastewater and impaired hygiene, and indirectly by creating stress and social conflict, and undermining subsistence gardening and medical self-care. However, our study also illustrates how grassroots-led responses to the COVID-19 crisis address these vulnerabilities and identify priorities for managing water to support well-being. The results demonstrate two ways that subjective perceptions of well-being can help to promote resilience: first, by identifying stressors that undermine community well-being and adaptive capacity; and second, by voicing community experiences that can help to guide crisis responses and initiatives critical for adapting to social-ecological shocks. The results have important implications for enabling transformative change that aligns efforts to address issues linked to poverty and inequality with those seeking to respond to environmental emergencies.