There is still a great lack of information regarding spatial and temporal gradients of quantitative guild composition of the fish fauna and their relation to environmental variables in European estuaries. To fill parts of this gap in knowledge, fish species densities in the Elbe estuary were estimated with high resolution using samples taken by a commercial stow net vessel monthly between April 2009 and October 2010. Altogether, 61 fish species as well as cyprinid hybrids were recorded. A high number of these species belong to the marine life cycle categories of marine stragglers and marine estuarine-opportunists. However, all marine species contributed only 0.4 % to mean total fish abundance, whereas the anadromous species reached a proportion of more than 98 %. The total contribution of freshwater species to the overall catch was 1.4 %. The mean total fish abundance was about 362,989 individuals 10−6 m−3 between April 2009 and October 2010. According to their abundance proportions, the fish fauna was dominated by the following three species: Osmerus eperlanus (96.1 %), Alosa fallax (1.9 %), and Gymnocephalus cernua (0.9 %). Twenty-nine percent of the species had a boreal distribution and 27.4 % belonged to the lusitanian distribution category, whereas a minority of 3.2 % of the species were of Atlantic origin. An additional 40.4 % of the species were freshwater species which were divided into the following five zoogeographical categories: European (19.3 %), Euro-Siberian (8.1 %), Holarctic (6.4 %), Nordic (3.3 %) and Pale-Arctic (3.3 %). The species composition underwent interannual changes comparing both years of investigation at each of the sampling sites in the Elbe estuary. Using the Bio-Env analysis, the maximum correlation between fish assemblage structure and environmental variables was obtained for a parameter combination comprising salinity, water depth, water temperature, and oxygen concentration.