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Epiphytes on seagrass (Zostera marina) growing in the lower intertidal were examined along an estuarine gradient within Yaquina Bay, Oregon over a period of 4 years. The Yaquina Estuary receives high levels of nutrients from the watershed during the wet season and from the ocean during the dry season. Mean epiphyte biomass per unit seagrass leaf surface area (epiphyte load) peaked during the summer, and thus epiphyte load was higher during dry season than wet season in both marine and riverine dominated regions. Epiphyte load was greater in marine than in riverine dominated areas in both wet and dry seasons, although only dry season differences were significant. There was no evidence that grazers controlled epiphyte load differences. Annual DIN concentration was inversely related to epiphyte load, principally because of elevated wet season dissolved inorganic nitrogen from river inputs. While there was a positive annual relation of epiphyte load to PO4 concentration, it is not clear that phosphorus becomes a limiting nutrient for epiphyte growth. Water column light attenuation tends to increase linearly with distance from the estuary mouth, while both epiphyte load and Z. marina biomass tend to decrease. Both seagrass and seagrass epiphytes may be increasingly light limited in the upper estuary, and thus, epiphyte loads may have proportionally more impact on seagrass occurrence in this estuarine region.