Copper biogeochemistry is largely controlled by its bonding to natural organic matter (NOM) for reasons not well understood. Using XANES and EXAFS spectroscopy, along with supporting thermodynamic equilibrium calculations and structural and steric considerations, we show evidence at pH 4.5 and 5.5 for a five-membered Cu(malate)2-like ring chelate at 100–300 ppm Cu concentration, and a six-membered Cu(malonate))1–2-like ring chelate at higher concentration. A “structure fingerprint” is defined for the 5.0–7.0 Å−1 EXAFS region which is indicative of the ring size and number (i.e., mono- vs. bis-chelate), and the distance and bonding of axial oxygens (Oax) perpendicular to the chelate plane formed by the four equatorial oxygens (Oeq) at 1.94 Å. The stronger malate-type chelate is a C4 dicarboxylate, and the weaker malonate-type chelate a C3 dicarboxylate. The malate-type chelate owes its superior binding strength to an –OH for –H substitution on the α carbon, thus offering additional binding possibilities. The two new model structures are consistent with the majority of carboxyl groups being clustered and α-OH substitutions common in NOM, as shown by recent infrared and NMR studies. The high affinity of NOM for Cu(II) is explained by the abundance and geometrical fit of the two types of structures to the size of the equatorial plane of Cu(II). The weaker binding abilities of functionalized aromatic rings also is explained, as malate-type and malonate-type structures are present only on aliphatic chains. For example, salicylate is a monocarboxylate which forms an unfavorable six-membered chelate, because the OH substitution is in the β position. Similarly, phthalate is a dicarboxylate forming a highly strained seven-membered chelate. Five-membered Cu(II) chelates can be anchored by a thiol α-SH substituent instead of an alcohol α-OH, as in thio-carboxylic acids. This type of chelate is seldom present in NOM, but forms rapidly when Cu(II) is photoreduced to Cu(I) at room temperature under the X-ray beam. When the sample is wet, exposure to the beam can reduce Cu(II) to Cu(0). Chelates with an α-amino substituent were not detected, suggesting that malate-like α-OH dicarboxylates are stronger ligands than amino acids at acidic pH, in agreement with the strong electronegativity of the COOH clusters. However, aminocarboxylate Cu(II) chelates may form after saturation of the strongest sites or at circumneutral pH, and could be observed in NOM fractions enriched in proteinaceous material. Overall, our results support the following propositions: (1) The most stable Cu–NOM chelates at acidic pH are formed with closely-spaced carboxyl groups and hydroxyl donors in the α-position; oxalate-type ring chelates are not observed. (2) Cu(II) bonds the four equatorial oxygens to the heuristic distance of 1.94 ± 0.01 Å, compared to 1.97 Å in water. This shortening increases the ligand field strength, and hence the covalency of the Cu–Oeq bond and stability of the chelate. (3) The chelate is further stabilized by the bonding of axial oxygens with intra- or inter-molecular carboxyl groups. (4) Steric hindrances in NOM are the main reason for the absence of Cu–Cu interactions, which otherwise are common in carboxylate coordination complexes.