Five new metal–organic compounds of formula A_n[Cu(mal)₂(H₂O)_m] (A being an amine cation and H₂mal = malonic acid) have been structurally and magnetically characterized. The crystal structure of these compounds consists of an alternation of malonate-containing copper(II) anionic and amine cationic layers. Depending on the amine cation, the bis(malonate)cuprate(II) units can be connected to other units through carboxylate bridges resulting in anionic networks which exhibit different topologies: monomers (2 and 5), layers (3 and 4) and three-dimensional structures (1). Hydrogen bonding plays an important role in the self-assembling of metal–organic compounds and how the size of the amine cation, in this case, can control the malonate-bridged copper(II) structure and moreover can tune the magnetic properties of these compounds. Variable-temperature (1.9–290 K) magnetic susceptibility measurements indicate the occurrence of weak ferromagnetic interactions [+0.263(5) and +0.755(1) cm⁻¹] between the copper(II) ions through the anti–anti caboxylate–malonate bridges.