Abstract Rock mechanical properties are of key importance in coal mining exploration, coal bed methane production and CO2 storage in deep unmineable coal seams; accurate data is required so that geohazards (e.g. layer collapse or methane/CO2 leakage) can be avoided. In this context it is well established that coal matrix swelling due to water adsorption significantly changes the coal microstructure. However, how water adsorption and the associated with microstructural changes affect the mechanical properties is only poorly understood, despite the fact that micro-scale mechanical properties determine the overall geo-mechanical response as failure initiates at the weakest point. Thus, we measured nanoscale rock mechanical properties via nanoindentation tests and compared the results with traditional acoustic methods on heterogeneous medium rank coal samples in both dry and brine saturated conditions. The microscale heterogeneity of the rock mechanical properties was mapped and compared with the morphology of the sample (measured by SEM and microCT). While the nanoindentation tests measured decreasing indentation moduli after water adsorption (−60% to −66%), the traditional acoustic tests measured an increase (+17%). We concluded that acoustic tests failed to capture the accurate rock mechanical properties changes for the heterogeneous coal during water adsorption. It is thus necessary to measure the coal rock mechanical properties at the microscale to obtain more accurate data and reduce the risk of geohazards.