Ephemeral aquatic environments are important habitats for a variety of species. They are highly variable with regards to vegetation structure and physico-chemical features that potentially mediate outcomes of biotic interactions. Multiple environmental variables and their emergent impacts on the relationship between prey consumption rate by a predator and prey density (functional response), however, are rarely assessed. Here, we investigated the combined effects of temperature and habitat complexity on the functional response of the freshwater predatory notonectid Enithares sobria on the cladoceran prey organism Daphnia longispina. A Type II functional response was observed for E. sobria predating on D. longispina and while temperature and habitat complexity had no effect on the response type, these environmental variables interacted with consequences for the magnitude of the functional responses. Overall, structural complexity favored the predator as greater consumption was observed in the most complex habitat treatment. Temperature effects were also evident although these effects were not unidirectional with regard to treatment factor gradients as predators were the most successful at intermediary temperatures. Furthermore, there was a complex interplay between habitat complexity and temperature, with attack rates being greatest at low and high complexities within intermediate temperatures, while at zero complexity attack rates were greatest at the lowest temperature. The effect of habitat on handling times was only evident in the low temperature treatments which decreased steadily with each increase in complexity. Through the application of functional responses the synergistic effects of multiple environmental drivers on predator–prey interaction outcomes have been highlighted, adding insight into how interactions among species may be affected by natural or artificially induced environmental variability.