Understanding the effects of biodiversity declines on communities and ecosystems is one of the current grand challenges in ecology. Much research has been devoted to quantifying the effects of species loss from primary producer communities and multi-trophic communities in mesocosms, but less is known about the effects of species loss from food webs from multi-trophic communities. Studies that quantify species loss from multi-trophic communities in the field rely on observational data of populations to infer changes in the interactions between species. However, there is a lack of field data that uses direct observations of species interactions to quantify the effects of species loss on multi-trophic communities. This collection of studies utilizes stable isotopes as well as gut analyses combined with population data to quantify the effects of amphibian declines in highland Panamanian streams on food web structure of an insect-algal community. Results showed that the loss of amphibians can result in changes of resource use by grazing insect genera, but not necessarily lead to changes in their abundance. Furthermore, amphibians had a role in structuring the diatom community that grazing insects could not duplicate, providing insight for why grazing insects did not functionally compensate for grazing tadpoles. Lastly, structure of the whole food web was more resilient to species loss than expected based on models that assume fixed trophic linkages due to a reorganization of the food web, which was driven by shifting resource use and the presence of generalist consumers that immigrated into the community following amphibian declines. These studies showed shifts in resource use within individual populations, but not shifts in the topology of the whole food web, suggesting changes in food web structure maybe more detectable at finer scales, e.g. individual populations, rather than coarser scales, e.g. the whole food web. Additionally, these results highlight the potential immigrant species may have for affecting food web topology following a species loss. Together, these studies provide empirical insight into how species loss can affect food webs, challenging theoretical predictions and providing a framework for future food web research.