Non-consumptive effects (NCEs) of predators owing to induced changes in prey traits are predicted to influence the structure of ecological communities. However, evidence of the importance of NCEs is limited primarily to simple systems (e.g. two to four species) over relatively short periods (e.g. less than one generation). We examined the NCEs of a fish predator, arising from phenotypic plasticity in zooplankton prey traits, over multiple generations of a diverse zooplankton community. The presence of fish, caged to remove consumptive effects, strongly influenced zooplankton community structure, through both direct and indirect NCE pathways, altering the abundance of many taxa by magnitudes as large as 3 to 10-fold. Presence of fish affected different species of cladocerans and copepods both positively and negatively. A particularly striking result was the reversal of dominance in copepod taxa: presence of fish reduced the ratio of calanoids to cyclopoids from 6.3 to 0.43. Further, the NCE of fish had a strong negative trophic cascade to zooplankton resources (phytoplankton). To our knowledge, this is the first experiment to show that NCEs can influence the abundance of multiple prey species over time spans of multiple prey generations. Our findings demonstrate that adaptive phenotypic plasticity of individuals can scale-up to affect the structure of ecological communities.