Estuarine zonation and community assemblages are frequently correlated with salinity, although the extent or nature of this correlation varies considerably among the published studies. While a smooth transition in biological communities is often conceptualized in association with estuarine fresh, brackish, and marine conditions, many studies have shown more distinct communities and the altogether absence of a brackish community. We explore these viewpoints in light of plant observations and soil and aquatic microbial analyses from permanent plots established on the Elbe River Estuary of northern Germany. Generally, two distinct communities were observed, a polyhaline assemblage towards the mouth of the system, and another that was associated with both the fresh and brackish mesohaline regimes further upriver. This was most pronounced among plant and soil bacteria communities, while aquatic 16S assemblages reflected little distinction at all. The proportion of marine classified taxa declined from the mouth to upriver and suggests that while the transition from marine to brackish or fresh vegetation falls within the sampled area, the same transition for microbial taxa could not be observed and may be further upriver. Thus, although we were able to identify two distinct communities, the limit of marine taxa was only evident for vegetation. While tidal and weather-related hydrology, as well as soil properties were also influential in distinguishing the communities, much of the variance remains unexplained. Further sampling, classification, and partitioning is necessary to determine the origin and/or autochthonous habitat, if any, for the Elbe River estuarine taxa.