High-latitude boreal and arctic surface/inland waters contain sizeable reservoirs of dissolved organic matter (DOM) and trace elements (TE), which are subject to seasonal freezing. Specifically, shallow ponds and lakes in the permafrost zone often freeze solid, which can lead to transformations in the colloidal and dissolved fractions of DOM and TE. Here, we present results from experimental freeze-thaw cycles using iron (Fe)- and DOM-rich water from thaw ponds situated in Stordalen and Storflaket palsa mires in northern Sweden. After ten cycles of freezing, 85% of Fe and 25% of dissolved organic carbon (DOC) were removed from solution in circumneutral fen water (pH 6.9) but a much smaller removal of Fe and DOC (< 7%) was found in acidic bog water (pH 3.6). This removal pattern was consistent with initial supersaturation of fen water with respect to Fe hydroxide and a lack of supersaturation with any secondary mineral phase in the bog water. There was a nearly two- to threefold increase in the low-molecular-weight (LMW) fraction of organic carbon (OC) and several TEs caused by the repeated freeze-thaw cycles. Future increases in the freeze-thaw frequency of surface waters with climate warming may remove up to 25% of DOC in circumneutral organic-rich waters. Furthermore, an increase of LMW OC may result in enhanced carbon dioxide losses from aquatic ecosystems since this fraction is potentially more susceptible to biodegradation.