Salt marshes, eelgrass beds (Zostera marina), and benthic macroalgae frequently occur in close proximity along the steep tidal channels of Pacific Northwest estuaries, where they constitute distinct patches of transitional land-margin habitat. The eelgrass beds and adjacent salt marshes within the South Slough National Estuarine Research Reserve, Oregon, provide an opportunity to investigate commonalities and differences between two ecological-indicator communities that are often separated by only a few meters. The principal objectives of this study are to establish a series of adjacent eelgrass and salt marsh assessment and monitoring sites within different hydrographic regions of the South Slough estuary and to characterize initial temporal and spatial changes in the composition of the plant communities in accordance with new field protocols developed by the National Estuarine Research Reserve System (NERRS) and by SeagrassNet. Eelgrass beds and emergent salt marsh communities were sampled at three study sites located along the estuarine gradient of the South Slough (43°20′N, 124°19′W). Study sites were established at (1) Collver Point (marine-dominated region), (2) Valino Island (polyhaline region), and (3) Danger Point (riverine/mesohaline region). Ambient water parameters and water column nutrients were monitored throughout the study period (2004–05) as part of the South Slough NERR System-Wide Monitoring Program. Periodic assessment of Rod Sediment Elevation Table (RSET) stations established within the eelgrass beds revealed that surface elevation increased at a rate of about 0.84 mm mo−1 at the Valino Island site but decreased at a rate of about 0.44 mm mo−1 at the Danger Point study site. Metrics of community richness, diversity, and species equitability indicate that the adjacent salt marshes and eelgrass beds develop community characteristics within the South Slough that are strongly reflective of their location along the estuarine gradient. The community composition, spatial cover, and density of macrophytes within the salt marsh and eelgrass communities were very similar between the Collver Point and Valino Island study sites, where mean monthly salinities in the tidal channel ranged between 25 and 32, and water temperatures were moderate (10–16 °C) throughout the year. In contrast, the salt marsh communities and eelgrass beds were distinctly different at the Danger Point study site, where mean monthly salinities ranged between 10 and 20, and water temperatures were much warmer in summer (20 °C) than in winter (9 °C). These intertidal salt marshes and eelgrass beds are highly productive and ecologically important components of the South Slough estuarine ecosystem despite their low richness of macrophyte species and relatively low metrics of community diversity. Recognition of these landscape-level differences in composition and productivity of submersed and emergent vegetation is important in the South Slough because the plant communities have potential to serve as reference sites to gauge the effectiveness of off-site habitat restoration and enhancement efforts.