Musa Estuary is one of the most valuable aquatic ecosystems in the in Khuzestan Province. Previous studies on sediment and organisms in this ecosystem found some indications of mercury pollution in this area and have emphasized that mercury concentrations are above global standards. The aim of this study was to evaluate the mercury concentration in the waters of Musa Estuary. For this purpose, five creeks (Zangi, Jafari, Petroshimi, Ghazaleh and Majidieh) of Musa Estuary were investigated. Water samples were collected in November 2009. The extraction of dissolved mercury from water samples were conducted according to the APHA standard method and the level of Hg were determined using cold vapor atomic absorption spectrometry. Mercury concentrations in water samples ranged from 3.66 to 12.00 μg/l. The highest Hg concentrations were observed in at Ghazaleh and Majidieh creeks and the lowest mercury contents were found in Zangi creek. The results of this study indicated that Hg concentration in waters of Musa Estuary exceeds the maximum acceptable level (0.2 μg/l) and warning limit (2.0 μg/l) for mercury in seawater which is a critical environmental issue for this region.