Extensive nanoindentation testing over a range of deflection depths of up to 4 μm yielded a large dataset, providing a viable framework for the statistical assessment of the mechanical properties, specifically elastic modulus (E) and hardness (H), of compositionally diverse organic-rich mudstone samples. The data from indentations as shallow as 300–400 nm were clustered using the k-means algorithm to identify three mechanical categories in the samples: a soft pseudophase (e.g., organic matter, gypsum, and clay minerals), a stiff pseudophase (e.g., quartz and feldspar), and a transitional composite-like pseudophase bridging the soft and hard minerals. The initially diverse values of E and H for the mechanical pseudophases were observed to converge to a constant value at indentations beyond 2–2.5 μm (varying between different samples), implying the existence of a minimal probing depth for assessing the bulk E and H of heterogeneous mudstone samples. The obtained bulk E and H values (8–21 GPa and 0.3–0.9 GPa, respectively) demonstrated a strong correlation with the mineralogical composition of the indented samples. Despite containing a notable proportion of mechanically stiff components (>45 vol%), the bulk mechanical parameters determined in this study were significantly lower than those reported for major shale formations such as the Barnett and Longmaxi Shale. This discrepancy is primarily due to the presence of organic matter with low thermal maturity (Ro < 0.6%), which constitutes <36 vol% of the samples, and a significant gypsum content, accounting for <15 vol%. The employed approach not only demonstrated the importance of choosing the proper indentation depths for investigating the mechanical properties of highly heterogeneous mudstone rocks and their constituent minerals, but it also illustrated the capability of examining various volumes of investigation using nanoindentation, approaching macroscopic values, and identifying a representative element volume (REV). The findings also provided crucial insights into the fracability and overall producibility of the investigated formations, thereby enhancing our understanding of their extraction potential. •CSM nanoindentation assesses macro-scale rock mechanics, surpassing nano- and micro-scale norms.•Indentation depths over 2.5 μm capture representative element volume (REV) in heterogeneous rock samples.•The findings highlighted the significant influence of rock composition on its mechanical properties.