The state of Michigan has approximately 16,000 km of cold water stream habitat, supporting biodiversity, improving water quality, and acting as a refuge to temperature sensitive fish species in a warming climate. However, because of climate change, cold water streams in the state are at risk along with many of their associated aesthetic, regulating, supporting, and provisioning services. To support cold water stream resilience, managers need information on the spatial and temporal variability in key water quality parameters including temperature, dissolved oxygen (DO), and specific conductance. We deployed AquaBOT, an aquatic drone developed by Oak Ridge National Laboratory, along the Muskegon River in Michigan to monitor spatial changes in water quality during summer 2024. AquaBOT allowed the team to collect hundreds of observations along a river course and navigate to tributary mouths to document water quality from contributing sub-watersheds. We observed changes in shallow water temperature (min: 14.9°C to max: 21.7°C), DO (min: 6.6 mg/l to max: 10.7 mg/l), and specific conductance (min: 339.8 μS/cm to max: 431.4 μS/cm) from tributary and groundwater contributions. The detailed spatial maps of water quality that resulted will aide in decision-making for stream restoration efforts and provide a pathway for gathering low cost high spatial resolution data to inform protection and restoration plans in other impacted watersheds.