Variation in the availability and quality of food sources for primary and secondary consumers shapes how nutrients enter and move through river food webs. In the nitrogen-limited South Fork Eel River (SFER), Cladophora glomerata dominates primary producer biomass during the summer growing season and, through colonization by epiphytic diatoms, becomes a key energetic and nutritional resource for consumers. In this study, we assessed microbial community composition associated with three nutritionally distinct successional stages of Cladophora (early green, middle yellow, and late red) in the SFER using 16S and 18S rRNA amplicon sequencing. We then used stable isotope tracing (13C & 15N) to measure primary productivity and subsequent transfer of fixed Carbon (C) and nitrogen (N) to turf-weaving midges (Pseudochironomus richardsonii; a dominant grazer) and onward to aeshnid larvae (Aeshna walkeri; a common predatory macroinvertebrate) across the three stages of Cladophora differing in epiphyte load. Algae, midges, and predators were incubated in flow through buckets in a shallow open river reach for eight days with six replicates per successional stage. C- and N-fixation were primarily controlled by Cladophora successional stage. The red stage exhibited higher mass-specific N-fixation rates than earlier stages (green< yellow< red), whereas mass-specific C-fixation declined from green to red stage Cladophora (green> yellow> red). C and N transfer to midges and aeshnids was also dependent on Cladophora successional stage and was greatest for the late stage Cladophora. Sequencing results suggest that these differences were driven by microbial variation, with red-stage Cladophora supporting a higher diversity and abundance of diazotrophic epiphytic diatoms (e.g., Epithemia). Together, these findings suggest that Cladophora stages differentially contribute to upward trophic transfer, with later stages pushing more C and N up the food chain because of Cladophora’s association with microbial partners. This study highlights the central role of seasonal algal variation and algal-diatom associations in regulating algal quality, nutrient cycling and energy transfer to consumers in stream food webs.