Two new layered copper hybrid materials, namely, the copper thiophene-2,5-diphosphonate [Cu2(H2O)2(O3P–C4H2S–PO3)] (Pnma; a = 7.525 Å, b = 18.292 Å, c = 7.520 Å) and the copper 3-fluorophenylphosphonate Cu(H2O)PO3–C6H4F (P21/c; a = 14.305 Å, b = 7.550 Å, c = 7.479 Å, β = 92.32°), have been synthesized. These compounds belong to the large homologous Cu(H2O)PO3R/[Cu2(H2O)2(O3P–R–PO3)] series, the structure of which is dictated by the presence of isolated dimeric pyramidal Cu2O6(H2O)2 units. The role of the Cu/H2O molar ratio of 1 in the stabilization of such a structure is discussed in connection with the Jahn–Teller effect of the copper cation. The study of the magnetic behavior of polycrystalline samples of the two compounds has revealed antiferromagnetic coupling between the copper ions. The interactions within the dimeric unit were estimated by the Bleaney–Bowers law with the spin Hamiltonian H = –JSCu1SCu2 + gβHS: J = –6.27 cm–1 for [Cu(H2O)PO3]2C4H2S, and J = –6.07 cm–1 for Cu(H2O)PO3–C6H4F.