Anthropogenic activities constitute a major threat to the physical and ecological integrity of freshwater ecosystems. Among the various anthropogenic impacts, alterations in land use and occupation patterns stand out as key drivers of aquatic ecosystem degradation and loss. In this context, agroforestry systems stand out among various land uses as an alternative for reducing environmental impacts. This study evaluated the integrity of streams in the Atlantic Forest under different land use types and their effects on dragonfly larval assemblages. Dragonfly larvae were collected in native forests, pastures, and cocoa cultivation areas, known locally as Cabruca (an agroforestry system in which Atlantic Forest trees are partially preserved, and cacao is planted in the understory). Our results revealed a difference in genus richness among the studied areas, with Cabruca areas showing higher richness and pasture areas exhibiting lower richness. We also observed variations in species composition, with native areas displaying a more homogeneous composition and pasture areas exhibiting a more heterogeneous composition. In addition, our results indicated that dragonfly larvae can serve as excellent indicators of sustainable cultivation areas. Although Cabruca areas represent a model of sustainable agriculture with the potential to contribute to biodiversity preservation, this study emphasizes that such areas cannot fully replace native habitats, reiterating the importance of conserving the remaining forests and their biodiversity.