The chemical composition of river waters represents an important matter of investigation to understand environment modifications in response to climate changes and global warming. Prolonged dry periods, heavy flood events, degradation of the lands and ice thawing, modify the chemical composition of river waters influencing the drivers governing the complex dynamics of river catchments where everything comes together. In this framework, Compositional Data Analysis (CoDA) offers methods in which the complex structure of the river water composition and the interrelationships among the various components are put into the proper context for their statistical analysis. In this research, we propose a new CoDA approach combining the robust Mahalanobis distance (D) calculus of ilr-transformed chemical variables and the perturbation difference, both with respect to a pristine compositional benchmark. The aim was to trace the change in the chemical composition of the Eastern Siberian River Chemistry Database where degradation of the permafrost for global warming produces important effects on natural waters. The findings indicate complex multiplicative laws and feedback mechanisms governing solutes in Eastern Siberian rivers, with high values of D found where permafrost is more discontinuous. Perturbations clearly discriminate chemical components more resilient to stresses induced by global changes (Ca2+, Mg2+ and HCO3−) from those whose variability is not maintained under control (Cl−, Na+, SO42−). These outcomes open up a new scenario in searching for spatiotemporal resilience metrics to reveal rivers response to environmental changes.