Conversion to agriculture, habitat fragmentation, and the loss of native grazers have made tallgrass prairie one of the most endangered ecosystems. One management option for the remaining prairie parcels, patch-burn grazing (PBG), applies a controlled burn to a portion of the prairie to attract cattle, creating a mosaic of more- and less-grazed patches. Although beneficial to cattle and grassland birds, the potential impacts of PBG on streams have not been studied, and a holistic approach is needed to ensure against adverse effects. We used a Before-After-Control-Impact design to assess potential impacts of PBG with and without riparian protection on tallgrass prairie headwater streams. We sampled stream macroinvertebrates and benthic organic matter 2 yr before and 2 yr during PBG treatments on two grazed watersheds with riparian fencing (fenced), two unfenced grazed watersheds (unfenced), and two ungrazed (control) watersheds. Very fine benthic organic matter increased significantly (51%) in unfenced streams compared with controls ( < 0.007), and fine particulate organic matter (<1 mm and >250 µm) increased 3-fold in the unfenced streams compared with controls ( = 0.008). The contribution of fine inorganic sediments to total substrata increased 28% in unfenced streams during PBG, which was significantly different from controls ( = 0.03). Additionally, the abundance of Ephemeroptera, Plecoptera, and Trichoptera taxa decreased from 7635 to 687 individuals m in unfenced streams, which was significantly lower than in control streams ( = 0.008). Our results indicate that PBG adversely influences prairie streams through sediment inputs and reductions in sensitive invertebrate taxa, but riparian fencing can alleviate these impacts.