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Deforestation affects the ecological integrity of rivers and streams, threatening biodiversity and ecosystem services worldwide. However, few studies have strictly analyzed the effect of the functional responses of tropical streams to changes in forest cover since deforested basins are usually also influenced by confounding anthropogenic inputs. Here we address tropical streams and test whether the stable isotopic ratios of nitrogen (N, δ 15 N) and carbon (C, δ 13 C) and the ratio of C:N of ecosystem components vary along a forest cover gradient. We also assess the ecological integrity of streams by in situ measurements using physical features commonly used in stream quality assessments. The results showed that the δ 15 N of most aquatic components, δ 13 C of particulate matter and omnivorous fish, and C:N of particulate matter and algae vary significantly with forest cover, indicating the role of terrestrial vegetation in regulating stream biogeochemistry. The dual stable isotope analysis satisfactorily indicated the changes in terrestrial-aquatic connections regarding both N and C cycles, thus showing the role of algae and particulate matter in influencing stream fauna through food web transfers. Our results support the use of stable isotopes to monitor watershed deforestation and highlight the need for reassessment of the effects of anthropogenic inputs on δ 15 N increase in globally distributed inland waters since the loss of forest is a significant cause in itself., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)