Results from pilot studies on colloidal phase transport of newly deposited mercury in lake water and overland runoff demonstrate that the combination of ultrafiltration, and stable isotope amendment techniques is a viable tool for the study of mercury partitioning to filterable carbon. Ultrafiltration mass balance calculations were generally excellent, averaging 97.3, 96.1 and 99.8% for dissolved organic carbon (DOC), total mercury (Hg_T), and methylmercury (MeHg), respectively. Sub nanogram per liter quantities of isotope were measurable, and the observed phase distribution from replicate ultrafiltration separations on lake water agreed within 20%. We believe the data presented here are the first published colloidal phase mercury data on lake water and overland runoff from uncontaminated sites. Initial results from pilot-scale lake amendment experiments indicate that the choice of matrix used to dissolve the isotope did not affect the initial phase distribution of the added mercury in the lake. In addition there was anecdotal evidence that native MeHg was either recently produced in the system, or at a minimum, that this ‘old’ MeHg partitions to the same subset of DOC that binds the amended mercury. Initial results from pilot-scale overland runoff experiments indicate that less than 20% of newly deposited mercury was transported in the filterable fraction (<0.7 μm). There is some indication of colloidal phase enrichment of mercury in runoff compared to the phase distribution of organic carbon, but the mechanism of this enrichment is unclear. The phase distribution of newly deposited mercury can differ from that of organic carbon and native mercury, suggesting that the quality of the carbon (available ligands), not the quantity of carbon, regulates partitioning. Further characterization of DOC is needed to clarify the underlying mechanisms.