Midge larvae (Pseudochironomus richardsoni Malloch) in the South Fork Eel River, California, weave retreats in mats of Cladophora glomerata (L.) Kütz. and graze on its algal epiphytes. Densities of these midges and their effects on Cladophora vary over time (seasonally, over the course of succession, and interannually) and space (down the drainage network). New Cladophora growth is green, turns yellow with early colonization by a monolayer of Cocconeis, and rusty-red as it becomes heavily epiphytized by a multistory layer of Epithemia spp. (Rhopalodiaceae), diatoms that contain N-fixing endosymbiotic cyanobacteria. To determine how midges influence epiphyte assemblage structure, we incubated Cladophora in early (green [G]), mid (yellow [Y]), and late (rusty-red [R]) stages of succession with and without midges and assessed changes in epiphyte density and composition. Midge effects on epiphyte composition and density (as measured by % cover on Cladophora filaments) varied with stage of succession and proximity to the ends of midge retreats. Local increases in retreat-associated cyanobacteria occurred in Y and R stages. Percent cover of Cocconeis increased on Y filaments >2 cm from midge retreats (ambient) indicating indirect midge effects (e.g., fertilization). Midges were less effective grazers on adnate Cocconeis cells than on loosely attached Epithemia and often ingested Cladophora in the process of grazing or retreat building, especially in G and Y stages. In contrast, midges that grazed on R Cladophora primarily consumed diatoms in the Rhopalodiaceae. Midge survival and retreat quality were lower in G than in Y or R stages, where retreats were longer and denser. Shifts in epiphyte composition and % cover caused by midge–algae interactions at small scales (µm–m) could affect ecologically significant processes, such as N-fixation and foodweb interactions at larger reach and watershed scales.