The effects of cypermethrin, a commonly used pyrethroid insecticide, were studied in small in situ enclosures situatedin an eutrophic lake over an 11-day period. The experimental design used a regression principle that included threeuntreated controls and a gradient of six unreplicated cypermethrin concentrations, ranging from 0.01 to 6 mg/l. Thispaper is the second in a series of two and describes the effects on the species composition of the crustacean, rotifer,periphyton and phytoplankton communities. Multivariate ordination technique (redundancy analysis (RDA) combinedwith Monte Carlo permutation tests) showed that exposure to cypermethrin caused significant changes in the speciescomposition of the communities. Changes in the structure of the communities were observed following exposure to anominal concentration of 0.13 mg cypermethrin per litre above. The direct acute effect of exposure to cypermethrin wasa rapid decrease of many species of crustacean zooplankton. The alterations in crustacean species composition wereprobably due to variations in susceptibility to the direct toxic effects of cypermethrin. No effects concentration (NEC)for individual zooplankton species were calculated using inverse regression and revealed that copepod nauplii were themost sensitive (NEC /0.01 mg/l) of the crustacean groups examined. The observed alterations of the speciescomposition of the autotrophic communities as well as of the rotifers were most likely caused indirectly bycypermethrin, mediated through the direct negative effects of the insecticide on the crustacean grazers. The results ofthis experiment provide further knowledge about the direct and indirect effects of pesticide stress on the ecosystem level.They also show that there is a variation in sensitivity between different species of zooplankton under natural conditionsand thus exemplify the necessity of multispecies approaches in the risk assessment of pesticides.