Anthropogenic pressures are driving changes in eelgrass communities, which are altering baseline conditions in estuarine environments. Field detections have validated the transport of land-sourced pollutants to aquatic systems; however, studies rarely sample concurrently for pesticides, and pharmaceuticals and personal care products (PPCPs) across environmental compartments. Moreover, studies on contaminant uptake by eelgrass and associated species are even more limited. In collaboration with the Confederated Tribes of the Coos, Lower Umpqua and Siuslaw Indians (CTCLUSI), this study collected samples of water, eelgrass, clams, and sediment at sites of Tribal significance in Southern Oregon to test for organic contaminants (i.e., herbicides and pharmaceuticals). Paired sampling was conducted for analysis by the CTCLUSI in tandem with the United States Geological Survey (USGS) in order for the Tribe to develop analytical standards for future sampling efforts. Ten pesticides and eight pharmaceuticals were detected across the four sites, with the highest number of overall detections (27) at the Florence Marina site. The insecticide bifenthrin was most frequently detected across all media (0.012–1.565 μg/g organic carbon in sediment, 2.7–30 ng/g in organismal tissue) and the anti-diabetic agent metformin was the most detected PPCP in clam tissues (1.33–3.78 ng/g). Pesticides and PPCPs were observed to co-occur in eelgrass habitats, with numerous pesticide detections across media types. These findings demonstrate numerous routes of exposure for estuarine organisms which could be addressed with pharmaceutical disposal strategies or pesticide use restrictions near these habitats.