Three mononuclear coordination complexes of 1-butyl-2-((5-methyl-1H-pyrazol-3-yl)methyl)-1H-benzimidazole (L), namely [CoL]Cl₂ (C1), [Co₂L₂]Cl₂·H₂O (C2) and [Zn₂L₂]Cl₂ (C3), have been synthesized and characterized spectroscopically. Their single-crystal X-ray diffraction analysis revealed that C1 and C2 display pseudopolymorphism. The presence of N–H⋯Cl and C–H⋯Cl hydrogen bonding in the crystal structure of C1 and C3assists the formation of a 2D hydrogen bonded sheet and orthogonal packing [2D sheet + a pair of 1D chains], respectively, leading to supramolecular structures. A combination of N–H⋯Cl, C–H⋯Cl, O–H⋯Cl, and C–H⋯O interactions results however in a 2D corrugated hydrogen bonded sheet with inclusion of water molecules in C2. Hirshfeld surface analysis confirms that hydrogen bonding and π-stacking contacts stabilize the crystal structures. These metal complexes display good performance towards their antimicrobial activity against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. In particular a normalized minimum inhibitory concentration as low as 6.25 μg mL⁻¹ for the bacterial strains was recorded for C2. Its structure–bioactivity correlation is discussed in detail.