Indigenous peoples have been altering landscapes and coexisting with nature for millennia, but in the era of the Anthropocene, the advent of settler-colonialism and the conversion of lands through urbanization and agriculture has shifted the balance from coexistence to exploitation, severely impacting ecosystems. Stream ecosystems, particularly headwaters, are uniquely affected due to their reliance on energy inputs (i.e., carbon) from the landscape, which include dissolved organic matter (DOM) derived from terrestrial plant material. DOM is an important resource for stream microbiota, providing a critical carbon source for heterotrophy that influences community structure through the quantity and quality of inputs, that propagate upwards through the food web. Here we describe a novel stream assessment involving molecular and cultural indicators. At a regional scale (n=7), we showed DOM quality reflected land use more effectively than macroinvertebrates or decomposition. This effect was further investigated in the current study at a broader landscape scale in the highly settled province of Ontario, Canada (n=116), where DOM was significantly affected by land use and varied predictably with stream health. Explorations of stream health in Indigenous-managed watersheds use DOM as well as co-produced, culturally informed assessments to conduct biomonitoring in alignment with community values and priorities. In the post-2020 Global Biodiversity Framework, where Indigenous Peoples play a crucial role in its’ successful implementation, this research seeks to uplift and empower Indigenous knowledge and communities in the monitoring and care of freshwater.