Ecologists have long studied the effect of predators on prey population abundance while evolutionary biologists have measured prey trait evolution in response to predation. Ecological and evolutionary processes were generally thought to occur on different time scales, but recent evidence suggests that evolution may alter the ecological effects of predation over the course of ecological experiments. We used a protozoan and its mosquito-larvae predator, naturally found in the water-filled leaves of pitcher plants, to examine the effect of prey evolution on predator-prey interactions. In experiments conducted over 12 days (approximately 50 prey generations, but less than one predator generation), we measured a decrease in the effect of mosquito larvae predators on protozoa prey populations. In a separate set of experiments, we found that the presence of predators corresponded with evolution of smaller cell size and increased population growth rate. In ecological experiments, two situations commonly occur: strong selection pressure applied by the treatment itself and discrepancies in generation times of associate species. Our results suggest that in either situation, the resulting evolutionary patterns may lead to dramatic and important changes in ecological effect size.