We investigate the structures of H(3)Co(CN)(6) and D(3)Co(CN)(6) and their temperature dependence using a combination of advanced neutron and x-ray diffraction techniques. Lattice parameter refinements show marked temperature- and isotope-dependent effects in the thermal expansion behaviour. Reverse Monte Carlo modelling of neutron total scattering data characterizes the distribution of D atom positions in the deuterated compound; analysis of these distributions reveals that the two N-H/D bonds become increasingly different with increasing temperature, suggesting a mechanism for the observed thermal expansion anomalies. We discuss these results in the context of the previous crystallographic, spectroscopic and theoretical results for H(3)Co(CN)(6) and 'super-short' N···H···N systems in general.