Estuaries are characterized by a longitudinal salinity gradient. This gradient is one of the main environmental factors responsible for the distribution of organisms. Distinguishing salinity zones is of crucial importance, e.g., for the development of tools for the assessment of ecological quality. The methods most often applied for classifying water according to salinity are the Venice System and the method of Bulger et al. (1993), both of which determine zone boundaries using species occurrences relative to mean salinity. However, although these methods were developed for homoiohaline waters, they have also been routinely applied to poikilohaline systems. I tested the applicability of both methods using salinity and macroinvertebrate data for the poikilohaline Elbe Estuary (Germany). My results showed that the mid-estuary distribution of macro-invertebrates is determined by variation in salinity rather than by mean salinity. Consequently, neither of the two methods is applicable for defining salinity zones in the Elbe Estuary. Cluster analysis combined with a significance test, by contrast, was a better tool for identifying the boundaries of salinity zones in poikilohaline systems. In many estuaries, such as the Elbe Estuary, a maximum turbidity zone (MTZ) develops, where suspended matter accumulates owing to circulation processes. It is assumed that the MTZ is a stressful environment with an excess of organic matter, high deposition rates, large variations in salinity, and dredging activities. Under such harsh conditions, populations might remain below the carrying capacity, and it is assumed that competition is of little importance, as predicted by the stress gradient hypothesis. I tested whether competition for food is important in the MTZ of the Elbe Estuary using stable isotope analysis of the macroinvertebrate community. The isotopic niches of no two taxa within a feeding group overlapped, which indicated different resource use and the absence of competition. The main reasons for the lack of overlap of isotopic niches were differences in habitat, feeding behavior, and migration behavior. The Elbe Estuary is nowadays highly industrialized and has long been subjected to a plethora of human-caused alterations. However, it is largely unknown what changes occurred in benthic communities in the last century. Hence, I considered taxonomic and functional aspects of macrobenthic invertebrates of the Elbe Estuary given in data from 1889 (most natural state), 1985 and 1986 (highly polluted state), and 2006 (recent state) to assess benthic community shifts. Beta-diversity analysis showed that taxonomic differences between the sampling dates were mainly due to species turnover, whereas functional differences were predominantly a result of functional nestedness. Species number (S), functional richness (FRic), and functional redundancy reached minimum values in 1985 and 1986 and were highest and rather similar in 1889 and 2006. The decline in FRic from 1889 to 1985/1986 was non-random, consistent with habitat filtering. FRic, functional beta diversity, and S data suggested that the state of the estuary from 1889 was almost re-established in 2006. However, the community in 1889 significantly differed from that in 2006 owing to species replacement. My results indicate that FRic and FR in 1889 could have promoted ecosystem resilience and stability.