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Because genes and phenotypes are embedded within individuals, and individuals within populations, interactions within one level of biological organization are inherently linked to interactors at others. Here, we expand the network paradigm to consider that nodes can be embedded within other nodes, and connections (edges) between nodes at one level of organization form “bridges” for connections between nodes embedded within them. Such hierarchically embedded networks highlight two central properties of biological systems: 1) processes occurring across multiple levels of organization shape connections among biological units at any given level of organization and 2) ecological effects occurring at a given level of organization can propagate up or down to additional levels. Explicitly considering the embedded structure of evolutionary and ecological networks can capture otherwise hidden feedbacks and generate new insights into key biological phenomena, ultimately promoting a broader understanding of interactions in evolutionary theory., Interactions are ubiquitous across biological systems. Modeling their consequences requires capturing how units are organized across biological scales: gene and protein interactions shape phenotypic traits within individuals, individuals are embedded within populations, populations within communities, and communities within ecosystems. Doing so reveals how indirect connections among units arise from the structure of connections at higher or lower levels of organization, and how effects at one level of the network propagate across neighboring levels.