The trans-[Cu₂L₂Cl₂] (1), and cis-[Cu₂L₂Cl₂]·H₂O (2) isomers of a diphenoxido bridged Cu₂O₂ core have been synthesized using a tridentate reduced Schiff base ligand 2-[(2-dimethylamino-ethylamino)-methyl]-phenol. The geometry around Cu(II) is intermediate between square pyramid and trigonal bipyramid (Addison parameter, τ = 0.463) in 1 but nearly square pyramidal (τ = 0.049) in 2. The chloride ions are coordinated to Cu(II) and are trans oriented in 1 but cis oriented in 2. Both isomers have been optimized using density functional theory (DFT) calculations and it is found that the trans isomer is 7.2 kcal mol⁻¹ more favorable than the cis isomer. However, the hydrogen bonding interaction of crystallized water molecule with chloride ions compensates for the energy difference and stabilizes the cis isomer. Both complexes have been converted to a very rare phenoxido-azido bridged trinuclear species, [Cu₃L₂(μ_1,1-N₃)₂(H₂O)₂(ClO₄)₂] (3) which has also been characterized structurally. All the complexes are antiferromagnetically coupled but the magnitude of the coupling constants are significantly different (J = −156.60, −652.31, and −31.54 cm⁻¹ for 1, 2, and 3 respectively). Density functional theory (DFT) calculations have also been performed to gain further insight into the qualitative theoretical interpretation on the overall magnetic behavior of the complexes.