Principal Component Analysis (PCA) was used to derive estuarine salinity zones based on field data on the salinity ranges of 316 species/life stages in the mid-Atlantic region (chiefly Chesapeake Bay and Delaware Bay species). Application of PCA to the data matrix showed that the structure underlying a diversity of salinity distributions could be represented by only five Principal Components corresponding to five overlapping salinity zones: freshwater to 4‰, 2–14‰, 11–18‰, 16–27‰ to marine. The derived salinity zonation showed both differences and similarities to the Venice System of estuarine zonation. However, unlike the static and essentially descriptive Venice System, the new method will allow researchers to establish biologically-relevant local salinity zones, and then develop hypotheses about the processes that give rise to the resulting patterns. Examples of this procedure are given for the mid-Atlantic region. The method used here may also be useful for studying distributions across other environmental gradients, such as temperature, pH, substrate, turbidity, vegetation, or latitude.