The total Hg and methyl Hg in waters and sediments, as well as particulate total Hg (PTHg), were analyzed to study their distribution and partitioning in the Danshuei River Estuary (DRE), northern Taiwan. TOC and grain size were also determined in the sediment samples. The dissolved total Hg (DTHg) in waters ranged from 24.0 to 45.8 ng/L. The dissolved methyl Hg (DMeHg) concentrations contributed 0.6–30.4% of the DTHg pool, with the higher percentage appearing in the upper estuary. The DMeHg concentration positively correlated with the Chl.a within the estuary, suggesting that phytoplankton plays an important role in influencing the DMeHg concentration. The partitioning results indicated that DTHg chiefly dominates the THg (DTH + PTHg) pool, especially at a salinity of >15 psu region. The value of partition coefficient, log(K_D), was within a range of 3.54 to 4.68, and the value linearly decreased with increasing salinity. The sediment total Hg (STHg) concentrations ranged from 80 to 379 ng/g, and most data exceeded the NOAA guidelines value (ERL < 150 ng/g), indicating that the DRE is contaminated with Hg. The STHg concentrations inversely and positively correlated with the grain size and TOC content, respectively, suggesting that sediment Hg distributions are strongly influenced by the both parameters.