Pools and riffles create a mosaic of habitats in streams that are colonized by unique assemblages of autotrophic and heterotrophic organisms. As a result, it can be challenging to derive accurate estimates of reach-scale activity from point measurements. In this study, we used stable isotope techniques (13C and 15N) to determine habitat-specific carbon (C) and nitrogen (N) fixation rates and combine those with areal standing stock measurements and percent cover estimates obtained from drone imagery to derive reach-scale estimates of C- and N-fixation in the South Fork of the Eel River, an N-limited ecosystem. The study was conducted in a 100-m reach (velocity 0-5 cm/s, depth 0.44 m, width 10 m, slope 0.0005, drainage area 125 km2) where the autotrophic base is dominated by Cladophora glomerata floating mats and their associated epiphyte assemblages including Epithemia turgida, a diatom with an N-fixing endosymbiont; shorter, benthic filamentous Cladophora turfs; epilithic algae; and moss. Analysis of drone imagery determined that Cladophora mats, turfs, epilithon and moss covered, 7%, 15%, 69%, and 9% of the reach, respectively. Similarly, patch-specific areal standing stocks were 200.0, 236.3, 223.2, and 170.0 g DM m-2 for Cladophora mats, turfs, epilithon and moss. Isotope analyses and sequencing are ongoing; however, initial estimates of mass-specific fixation rates were 28 µg N/g algae/hr and 300 µg C/g algae/hr for N- and C-fixation in Cladophora mats, which translates to areal rates of 0.07 g N/m2/day and 0.70 mg C/m2/day within the mats. Single-station estimates of metabolism derived from the diel oxygen measurements was approximating 1.5 g O₂/m²/day, suggesting that the Cladophora mats likely account for ~50% of the carbon fixed in the reach (~5x its areal coverage). These preliminary results suggest that Cladophora and its unique epiphytic community play a disproportionate role in carbon and nitrogen fixation in the South Fork of the Eel River.