<p>Small aquatic systems can be highly vulnerable to anthropogenic activities. One way to assess such impacts is through functional beta diversity and bioindicators such as Odonata larvae. Here, we investigated how local, landscape, and spatial variables drive the functional beta diversity of Odonata larvae in 29 Amazonian streams under different levels of human pressure. We hypothesized that water and habitat-related variables would better explain the functional beta diversity of Odonata larvae than landscape or spatial variables. We used nine functional traits and the abundance of 24 recorded Odonata genera to calculate functional beta diversity of their communities. A high functional beta diversity was observed among streams, likely reflecting variation in stream physical habitat structure. When evaluating the functional beta diversity separately for each suborder, this pattern was observed in Zygoptera, driven by habitat integrity and exposed soil. For Anisoptera, no relationship was observed, indicating that stochastic or unmeasured variables likely drove their beta diversity. Our results showed that the functional beta diversity of Odonata larvae was habitat-structured and depended on stream integrity, highlighting the importance of maintaining natural stream conditions to conserve biodiversity, especially for Zygoptera, which are more sensitive to habitat degradation.</p>