Temporal variations and regional distributions of dissolved nutrients and their elemental ratios in the Iranian coastal waters of the Southern Caspian Sea were investigated. The data were collected in 1996-97 (Phase I, as a background data and undisturbed ecosystem) and in 2005 (Phase II, as a disturbed ecosystem) at sampling points (from 10 to 100 m depths). In addition to the two main sampling exercises, additional sample collections were carried out during the period of 1994 to 2004 as a long-term study. This study showed that the dissolved inorganic nitrogen/dissolved inorganic phosphorus (DIN/DIP) ratios in the southern Caspian Sea vary within a very narrow range (4.47 to 5.78) within the euphotic and aphotic layers and is by one order of magnitude lower than what have been reported for several other marine ecosystems. Phytoplankton growth seems to be nitrogen limited while the levels of P and Si always remain high. Factor Analysis/Principal Component Analysis (FA/PCA) of the correlation matrix showed that the nitrogen compounds are associated with the main factor accounting for 25.7-26.2% of the total variance for both the sampling periods. During Phase I, the Chrysophyta were the major group, whereas during Phase II the proportion of Chrysophyta in the total community progressively decreased, while the other groups increased.