Effects of a chronic application of the herbicide Afalon (active ingredient linuron) on physicochemical conditions, decomposition of plant litter, and densities of zooplankton and macroinvertebrates were studied in indoor microcosms intended to model drainage ditches. For 28 days, concentrations of 0, 0.5, 5, 15, 50, and 150 micrograms/L linuron were maintained, each in two replicates. The microcosms were dominated by the macrophyte Elodea nuttallii. The functional response of the ecosystem is discussed in relation to shifts in community structure. Treatment effects of linuron on community metabolism, as a direct effect of the inhibition of the photosynthesis of macrophytes and algae, resulted in a decrease in dissolved oxygen and pH, and an increase in alkalinity and conductivity (NOEC 0.5 microgram/L). During the posttreatment period, differences between controls and highest dose fell gradually, but were still significant 7 weeks after the start of linuron application. Decomposition of particulate organic material in litter bags was not affected, despite decreases in DO. The negative effect of linuron on several algae (cryptophytes, diatoms) and the positive effect on the green alga Chlamydomonas resulted in a decrease of several Rotatoria and an increase in Copepoda, and, to a lesser extent, Cladocera. The complete disappearance of the macrophyte E. nuttallii in the 150 micrograms/L microcosms and a 50% reduction of its biomass in the 50 micrograms/L microcosms reduced the numbers of the snail Physella acuta, which normally inhabits macrophytes. Artificial substrates indicated a significant increase in the isopod Asellus aquaticus in the 50 and 150 micrograms/L microcosms during the post-treatment period. This, however, was counteracted by a significant decrease in A. aquaticus at the final harvest. Changes in the ecosystem structure (decline in macrophyte biomass) made the artificial substrates more attractive.