A catenated structure is formed through dynamic self-assembly of 1,3-bis(4-pyridyloxy)propane and cis-protected Pd(II) metal with ethylenediamine in water. H-1 NMR spectra have revealed that the formation of [2]catenane is dependent on the concentration of macrocyclic ring. We have performed the structural analysis of macrocyclic ring and [2]catenane using H-H COSY and ESI MS. The dynamic process of the catenation has been elucidated by van't Hoff plot and the formation of [2]catenane is enthalpically favored in D2O, strongly suggesting the hydrophobic interactions for the formation of [2]catenane. Diffusion-ordered NMR spectroscopy (DOSY) distinguishes between dinuclear self-assembled macrocyclic ring and [2]catenane, indicating that [2]catenanes diffuse slower than macrocyclic rings in D2O.