The annual spawning migrations of fishes such as salmonids and clupeids deliver millions of kilograms of labile resources to rivers and lakes globally. The delivery and cycling of carbon, nitrogen, phosphorus, and micronutrients from the excreta, gametes, and decomposing bodies of anadromous fishes such as Pacific salmon (Oncorhynchus spp.) is well documented in the literature. We have studied the ecological effects of Pacific salmon on spawning streams in their native (Southeast Alaska) and introduced (Laurentian Great Lakes) ranges. Stable isotopes and other metrics show that these nutrients permeate freshwater food webs and also penetrate riparian areas, but enhanced stream productivity is balanced by strong benthic disturbance imparted by spawning activities. Recent evidence suggests that adult salmon also transport contaminants in their bodies that are subsequently transferred to stream food webs. In the Great Lakes watershed, we demonstrate that several organic contaminants acquired in the lakes are concentrated in the bodies of salmon and then released into spawning streams and subsequently taken up by stream biota. For example, we have discovered that the emerging contaminant PFAS is maternally “offloaded” to salmon eggs during embryonic development thereby representing a potential conduit to resident stream fishes via egg consumption, similar to the transfer of other organic contaminants such as PCBs and DDE. This “dark side” of salmon subsidies has serious implications for both wildlife and humans that consume these fish, particularly for individuals reliant on this protein source. Such natural fish migrations are increasingly intersecting with emerging contaminants and therefore a more robust understanding of their coupled ecological and toxicological effects is needed.