The size-based forms of dissolved trace elements (TEs, < 0.45 μm) in ombrotrophic peatland waters have been investigated. Bog waters, and moss waters which were extracted from the living layer of Sphagnum mosses were studied. The size-based fractionation and analysis were accomplished using asymmetric flow field-flow fractionation hyphenated to ultraviolet visible detector and inductively coupled plasma mass spectrometry (AF4-UV-ICPMS). Ionic and small molecular species (< 0.5 kDa) were generally found in both waters for all TEs studied. Due to their small sizes, they were highly mobile and potentially bioavailable. The DOM-associated species include organic-TE complexes (< 1 kDa), Fe/Al-organic complexes (ca. 1.2 kDa), and organo-mineral colloids (2–5 kDa, e.g., nanoparticulate Fe/Al embedded in a humic-like organic matter). In the DOM-associated species, biologically essential elements (e.g., V, Co, and Cu) were mainly present in organic-metal complexes, while potentially toxic elements (e.g., As, and Pb) were primarily associated with Fe/Al-organic complexes and organo-mineral colloids. The inorganic particles were mainly found in moss waters, involving Al-bearing (ca. 6–7 kDa), Fe-bearing (25–35 kDa), and Th-bearing nanoparticles (12–15, and 64 kDa). The abundance of inorganic particles in moss waters reflected dust deposition in peatlands. The shift of size-resolved TE species was seen from inorganic to organic colloids and ionic species, suggesting the dissolution of dust during a long-term equilibrium with acidic bog waters.