1. We compared microbial biomass (bacteria, fungi, algae) and the activity of extracellular enzymes used in the decomposition of organic matter (OM) among different benthic substrata (leaves, coarse and fine substrata) over one hydrological year in a Mediterranean stream.
2. Microbial heterotrophic biomass (bacteria plus fungi) was generally higher than autotrophic biomass (algae), except during short periods of high light availability in the spring and winter. During these periods, sources of OM shifted towards autochthonous sources derived mainly from algae, which was demonstrated by high algal biomass and peptidase activity in benthic communities.
3. Heterotrophic activity peaked in the autumn. Bacterial and fungal biomass increased with the decomposition of cellulose and hemicellulose compounds from leaf material. Later, lignin decomposition was stimulated in fine (sand, gravel) and coarse (rocks, boulders and cobbles) substrata by the accumulation of fine detritus.
4. The Mediterranean summer drought provoked an earlier leaf fall. The resumption of the water flow caused the weathering of riparian soils and subsequently a large increase in dissolved organic carbon and nitrate, which led to growth of bacteria and fungi.