Ephemeral ponds are often dominated by species with both terrestrial and aquatic life phases. Such species have the potential to strongly alter the food web structure of ponds, particularly if they are predators. Here we experimentally tested the effects of salamander larvae (Salamandra salamandra) on invertebrate communities in ephemeral forest ponds. We repeatedly split two ponds into salamander enclosure- and exclosure-segments, and compared the diversity and biomass of potential prey organisms. We used stable isotopes of carbon (δ¹³C) and nitrogen (δ¹⁵N) of resources and consumers to characterise the food web structure. The presence of salamander larvae did not affect abundances of culicid larvae, their preferred prey. The population dynamics of most insect larvae was independent of the presence of salamander larvae, and was instead driven by the timing of hatching and emergence. However, a significant reduction resulting from salamander predation could be detected in the less abundant chironomid larvae. There was no substantial alteration of the food web structure as indicated by stable isotopes. However, the stable isotope results suggest a strong trophic subsidisation from the terrestrial system, which is probably the reason for the weak top-down effects of the salamander larvae on the invertebrate food web.