The complex chemistry of copper (Cu) in freshwater sediments at low concentrations is not well understood. We evaluated the transformation processes of Cu added to freshwater sediments under suboxic and anoxic conditions. Freshwater sediments from three sources in Michigan with different characteristics (Spring Creek, River Raisin, and Maple Lake) were spiked with 30 or 60 mg kg−1 Cu and incubated under a nitrogen atmosphere. After 28-d, each treatment subset was amended with organic matter (OM) to promote anoxic conditions and evaluate its effects on Cu speciation. OM addition triggered a shift from suboxic to anoxic conditions, and sequential extractions showed that Cu accordingly shifted from acid-soluble to oxidizable fractions. Extended X-ray absorption fine-structure (EXAFS) spectroscopy revealed that Cu sulfides dominated all anoxic samples except for Spring Creek 30 mg kg−1, where Cu(I) was predominantly complexed to thiol groups of OM. Covellite and chalcopyrite (CuFeS2) were the predominant Cu species in nearly all anoxic samples, as determined by Raman spectroscopy, scanning electron microscopy, and X-ray absorption near-edge structure (XANES) spectroscopy. Copper reduction also occurred under suboxic conditions: for two of three sediments, around 80% had been reduced to Cu(I), while the remaining 20% persisted as Cu(II) complexed to OM. However, in the third coarsest (i.e., Spring Creek), around 50% of the Cu had been reduced, forming Cu(I)-OM complexes, while the remainder was Cu(II)-OM complexes. Toxicity tests showed that survival of H. azteca and D. magna were significantly lower in suboxic treatments. Anoxic sediments triggered a near-complete transformation of Cu to sulfide minerals, reducing its toxicity.