The recognition of rapid eco-evolutionary feedback has spurred a paradigm shift in ecological theory in recent years. However, there remain few quantitative examples of how rapid evolution of a species can impact complex ecological systems, such as food webs, which in turn shape evolutionary pressures. Here, we leverage a long-term study of the eco-evolutionary feedbacks between rapid evolution of phenotypes in Trinidadian guppies on quantitative stream food web structures using ‘Isotracer,’ a Bayesan state-space mixing model approach for nitrogen isotope tracer experiments. Isotope tracer drip experiments were conducted 2-years post guppy introduction, but before evolution had occurred, and again at 10 years post-introduction when guppy phenotypes had evolved in the presence or absence of larger-bodied predatory fish. Prior to guppy evolution, we found similar food web structures and resource fluxes among sites. After the introduction, resource fluxes diverged with an increase in primary production and algal-driven flows through invertebrates in the predator reaches. Conversely, in the absence of predators, guppies reached larger sizes and consumed greater amounts of invertebrates, leading to top-down pressure on invertebrate prey and more detrital-sourced fluxes through the food web. This in turn altered dominant food web structures and flows resulting in a different primary and secondary production landscape to which additional evolutionary pressure occurs.