Electrospray ionization mass spectrometry (ESI-MS) is very often employed to study metal/ligand equilibria in aqueous solution. However, the ionization process can introduce perturbations which affect the speciation results in an unpredictable way. It is necessary to identify these perturbations in order to correctly interpret the ESI-MS speciation results. Aluminium(III)/1,6-dimethyl-4-hydroxy-3-pyridinecarboxylate (DQ716) aqueous solutions at various pH were analysed by ESI-MS, and speciation results were compared with those obtained by equilibrium techniques. Differences observed were both qualitative and quantitative. The ESI-MS spectral changes due to different settings of the following instrumental parameters were analyzed: the solution flow rate (F(S)), the nebulizer gas flow rate (F(G)), the potential applied at the entrance capillary (E(C)), and the temperature of the drying gas (T(G)). The effects produced by F(S) and E(C) on the spectra strongly suggest the key role of surface activity in determining the relative fraction of the ions reaching the detector. The experimental effects of F(S) and T(G) were interpreted considering the presence of at least two reactions in the gas phase and a dimerization occurring in the droplets. These perturbations cannot be generalized because they appear to be chemical system-related and instrument-dependent. Therefore, the identification of perturbations is a required task for any metal-ligand equilibrium study performed by ESI-MS. Our results indicate that perturbations can be identified by evaluating the effects produced in the spectra by a change of instrumental parameters.