Tropical rivers face increasing human pressures that fundamentally reshape human-river relationships. We estimated ecosystem metabolism in non-wadeable rivers in southern México with varying levels of human disturbance. In addition, we used the ecosystem metabolism concept to explore how communities perceive the condition of rivers and relate to these ecosystems. The smaller, less disturbed rivers draining forested catchments showed reduced gross primary production, ecosystem respiration, and net ecosystem production approaching autotrophy relative to larger and more disturbed catchments. The smaller rivers exhibited greater and sustained GPP during periods of low discharge and a more constrained metabolic fingerprint compared to larger and more disturbed rivers. We used an analogy with human metabolism to introduce the concept of ecosystem metabolism. Seasonal patterns in dissolved oxygen and ecosystem metabolism were shared with local communities in workshops to explore how local communities perceive river conditions and their connections to these ecosystems. Co-designed infographics, developed with community input, integrated ecological data with local knowledge, perceptions, and observations of how human activities affect river health. Interestingly, people can identify longitudinal zonation in minimally disturbed rivers based on water color and depth, while in the more disturbed sites, spatial zonation was not perceived. Historical changes in water quality and flow were also reported. Local people engaged in recreation, subsistence fishing and tourism at the forest rivers. In the more disturbed rivers, pollution restricts water use and fish consumption, while the increased abundance of crocodiles further limits recreational activities. We concluded that human pressures are causing profound changes in the ecology of tropical rivers. People can perceive these transformations, which may progressively undermine the resilience of human-river relationships.