There is increasing evidence that closely related species have contrasting ecosystem effects, but very little is known about the temporal scale of these effects. When organisms' ecosystem-effects persist beyond or emerge after their presence in the ecosystem, this might increase the potential for eco-evolutionary feedbacks to accompany evolutionary diversification. Here we studied lab-raised whitefish of a benthic-limnetic species pair from a postglacial adaptive radiation to test whether closely related species have contrasting effects on mesocosm ecosystems (hereafter ecosystem effects). We found that the presence of whitefish (ecological effect) had strong effects on some ecosystem components, for example by reducing snail and mussel abundance and increasing phytoplankton abundance. Whitefish species had contrasting effects (evolutionary effect) on benthic algal cover, dissolved organic carbon, and zooplankton community composition, but these effects only emerged several months after whitefish were removed from the ecosystem. The effects of plasticity and the interactive effects of species and plasticity were relatively weak and, with one exception, not significant. Ecological and evolutionary effect sizes were uncorrelated over both phases of the experiment, as were effect sizes between phases for both ecological and evolutionary contrasts. Overall, our results suggest that adaptive radiation can have effects on the structure and functioning of ecosystems, but that the temporal dynamics and mechanistic basis of these effects are insufficiently understood.