The mercury contaminated upper Penobscot Estuary in Maine provided a unique opportunity to rigorously examine the effect of sediment type and particle size on mercury concentrations in sediments, and to explain why sediments at different locations in the estuary had different mercury concentrations. This is because the Penobscot Estuary contains a large, well-mixed pool of mobile sediments of many different types (muds, sand, gravel, wood chips), which are the source of material for the permanently deposited surface sediments. Despite this mixing, average surface sediment mercury concentrations were very different in different locations, ranging from 238 ng/gdw to 1032 ng/gdw in the 11 subareas studied. Average total mercury concentrations were highly related to the type of sediment (wood chips > muds > sands) regardless of location in the estuary. The characteristics in both mobile and surface sediments that were positively related to total mercury concentrations were % organic matter (measured as loss on ignition) and %fines (measured usually as <62.5 μ). Also, in a subset of samples it was shown that mercury was positively associated only with the very finest (<44 μ) particles. Thus, side embayments of the estuary such as the Orland River and Mendall Marsh, which experience lower velocity currents and so accumulate more fine particles, tended to be much higher in mercury concentrations. This knowledge will be important in managing remediation of this system, as fine particles can be the most difficult to trap or to retain if dredging is employed. Methyl mercury was well correlated with total mercury and so its distribution would also be affected by transport characteristics. This was the case even in the mobile sediments, which were more oxic and not expected to provide a good habitat for methylation.