Ecosystem services do not exist independently from human perceptions and recognition. They are socially, culturally, economically, and environmentally scale- and context-dependent. Socio-cultural services tend to be difficult to evaluate and invisible to policymakers and conservation practitioners. Based on six years’ qualitative analysis of a floodplain fishery in the Pantanal wetland, Brazil, we bring an in-depth understanding of the socio-cultural ecosystem services in the region. We show that the inter- and intra-annual ecosystem dynamics variations in the flood pulse are closely associated with local people's governance structure, identity, and cosmological histories. All of them, to some extent, capture some of the unpredictable changes in the Pantanal. Our study uncovers part of the complex and rich social-cultural ecosystem service created from the interaction between local people and the ecosystem in which they are embedded. We also present the threats faced by these services in the face of current development projects in the Pantanal, such as the Waterway and Hydrometric Dams. We argue that the predicted outcome may jeopardize not only the social-cultural services in the Pantanal, but also the local people themselves and the environment that they are currently protecting.