Mercury (Hg) contamination, which includes its toxic byproduct monomethylmercury (MMHg), is ubiquitous and often severe in estuarine and near-shore systems of industrialized countries. However, Hg cycling is not well studied in anthropogenically impacted systems such as New York/New Jersey Harbor Estuary (NY/NJ Harbor), and more generally, knowledge concerning the biogeochemical cycling of toxic metals is limited for estuaries and coastal regions. Here, we are reporting results from a 1-year seasonally focused field investigation on the behavior and fate of Hg and MMHg in NY/NJ Harbor. Filtered (< 0.2-μm) and unfiltered reactive (labile) and total Hg, as well as filtered and particulate MMHg, were measured in surface and bottom waters (5–9 stations) in August 2002, February 2003, and May 2003. Scavenging by particulate matter is a major control on the partitioning of total Hg in the vertically well-mixed waters of the Harbor; 89–99% of total Hg (log K D = 5.3–6.5) and 56–89% of MMHg (log K D = 4.5–5.6) were in the particle phase. Mean levels of unfiltered total Hg (30–550 pM) and total MMHg (0.2–1.8 pM; filtered + particulate) were greater and more variable seasonally at the sites in Newark Bay and the Upper Harbor, as compared to the Lower Harbor and Jamaica Bay, consistent with fluvial inputs (Hudson River yields 90% of freshwater input) as a principal source of total Hg to the Harbor. Water-column particle-specific concentrations (mean ± SE) of total Hg (4.8 ± 0.5 nmol g − 1 ) and MMHg (20 ± 2 pmol g − 1 ; 0.4% of total Hg) are comparable to levels in surface sediment, suggesting significant sediment suspension and deposition. The major sources of total Hg (∼ 2440 mol y − 1 ) to NY/NJ Harbor are rivers (∼ 1640 mol y − 1 ; 67% of total inputs), the East River (∼ 630 mol y − 1 ), water pollution control facilities (WPCFs; ∼ 140 mol y − 1 ), and direct atmospheric deposition (∼ 30 mol y − 1 ). Although direct atmospheric deposition to NY/NJ Harbor is small, leaching (ca. 25–30% watershed delivery) of atmospheric Hg deposition to the NY/NJ Harbor watershed is a significant source (22–69%), but additional unknown sources also appear to contribute to fluvial Hg loadings. The MMHg flux to the Harbor from internal and external sources is estimated as 33 mol y − 1 with 18 mol y − 1 from rivers (55%), and 8 mol y − 1 (25%) from in situ sedimentary production and mobilization. While fluvial MMHg inputs are dominant, the relative source strength of watershed versus sedimentary riverine production is not yet clear.