Aptamers are single stranded nucleic acids with specific target-binding functionalities, biophysical and biochemical properties. The binding performance of aptamers to their cognate targets is influenced by the physicochemical conditions of the binding system particularly in relation to biomolecular charge distribution and hydrodynamic conformations in solution. Herein, we report the use of zeta potential measurements to characterise the surface charge distribution, biomolecular hydrodynamic size and the binding performance of a 15-mer thrombin binding aptamer (TBA) to thrombin under various physicochemical conditions of pH, temperature, monovalent (K+) and divalent (Mg2+) cation concentrations. Charge distribution analysis demonstrated time dependence in the formation of stable TBA-thrombin and TBA-thrombin-metal ion complexes. TBA was characterised to be most stable in pH above 9. The presence of monovalent and divalent metal ions reduced the electronegativity of TBA through electrostatic interactions, and this demonstrated to improve binding characteristics. TBA-thrombin complexes generated under different physicochemical conditions showed varying surface charge distributions. The stability of TBA-thrombin complex investigated using Scatchard analysis showed that the presence of K+ increased the binding performance by displaying a positive cooperativity relationship. The presence of Mg2+ showed a concave upward trend, potentially caused by heterogeneity in binding.