Floating algal mats can greatly increase aquatic insect emergence, both by enhancing insect production and providing partial refuge from aquatic predation. In a nitrogen-limited river subject to Mediterranean summer drought hydrology, the rate and composition of insect emergence from floating algal mats could be predicted from algal mat color, which in turn reflected dominant taxa of macroalgae and their diatom epiphytes. The rates of emergence by numbers (individuals day-1 500 cm-2) of Nematoceran flies were 3-25 times greater from yellow or rusty-colored Cladophora mats than from green Cladophora, Oedogonium, or Mougeotia mats with lower epiphyte densities. Biomass emergence from Cladophora mats that were rusty in color was 8-10 times greater than from yellow Cladophora mats, because larger Nematocerans dominated in rusty mats (Chironominae versus Ceratopogonidae in yellow mats). Yellow Cladophora mats were epiphytized by diatoms that were not nitrogen fixers (Cocconeis, Rhoicosphenia and Gomphonema), while rust-colored Cladophora mats were densely overgrown by Epithemia adnata (Kütz.) Bréb. and E. sorex Kütz., which both contain nitrogen-fixing cyanobacterial endosymbionts. Algal mat color in this system appears subject to successional and seasonal influences on epiphyte assemblages. Photogrammetric detection of colour changes in algal proliferations may help us track change in their ecological function.