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ABSTRACT ObjectiveApex-predator-initiated trophic cascades occur in many nearshore marine habitats that simultaneously serve as critical habitat and food sources for commercially and ecologically important species, including juvenile Pacific salmon Oncorhynchus spp. Yet the potential relationships among apex predators (e.g., sea otters Enhydra lutris), submerged aquatic vegetation, and juvenile salmonids are not well understood. In Southeast Alaska, we investigated (1) juvenile salmonid abundance in eelgrass Zostera marina meadows and understory kelp beds and (2) potential drivers of juvenile Chum Salmon Oncorhynchus keta and Pink Salmon O. gorbuscha abundance in eelgrass meadows. MethodsWe analyzed historic (1998–2007) beach seine surveys to compare juvenile salmonid abundance in nearshore habitats. We then employed the same survey (2017, 2019) in eelgrass to quantify juvenile salmonid abundance alongside the influence of sea otter density (number/km2), distance from anadromous stream (km), seasonality, sediment categorization, and aboveground eelgrass biomass (g/m2). ResultsWe found greater abundance of Chum Salmon in understory kelp compared with eelgrass, whereas Pink Salmon abundance was similar between habitats. In eelgrass, Chum Salmon abundance peaked in June and was positively associated with sea otter density. Pink Salmon abundance varied seasonally, peaking in May. We found increased Pink Salmon abundance with increasing sea otter density and distance from anadromous stream and decreased abundance with increased eelgrass biomass. ConclusionGrowth and survival while juvenile salmonids are out-migrating from streams and relying on nearshore vegetated habitats can determine if they recruit to fisheries as adults. Here, we highlight the use of multiple habitats, eelgrass and understory kelp, indicating that both should be explored as critical nursery habitat. We present evidence of indirect effects of sea otters influencing the abundance of juvenile salmonids, with potential further implications as sea otter populations expand. Apex predators, quality of vegetated habitats, and their structuring roles in the nearshore are critical for informing adaptive coastal fisheries management.