Connecting the discussions on resilience and governance of social-ecological systems (SESs) with the sociological analysis of social controversies, we explore a major red tide crisis on Chiloe Island, southern Chile, in 2016. Theoretically, we argue that controversies not only are methodological devices for the observation of the complex relations between nature and society in moments of crisis, but also are materially embedded in the SES dynamics and can work for or against systemic resilience. Empirically, we show that Chiloe's SES is an unstable regime prone to sudden shifts and identify the configuration of different lock-in mechanisms expressed in the reproduction of structural fragilities over the last three decades. From the examination of the social controversies on the 2016 red tide crisis, we draw several lessons. First, there is a complex interplay of visible and hidden fragilities of Chiloe's SES that, while being ignored or their resolution postponed to the future, materialize in the daily experience of inhabitants as a series of historical disappointments. Second, the unfolding of Chiloe's social-ecological crises involves epistemic disputes not only over concrete events but also on the very construction of the SES as a social-natural reality. In turn, this creates conditions for the emergence of strategic alignments between local, national, and transnational actors and shows the extent to which the socio-political articulation of knowledge may contribute to either improve or block the governance of the SES. Third, the social resources that came to light with the controversies reveal pathways for improving the governance regime of Chiloe Island's SES. This dimension highlights the normative relevance of commitments to recognize multiple scales of knowledge and articulate a plurality of actors in a nonhierarchical logic of cooperation.