Abstract Condition monitoring signals obtained from rotating machines often demonstrate a highly non-stationary and transient nature due to internal natural deterioration characteristics of their constituent components and external time-varying operational conditions. Traditional multivariate statistical monitoring approaches are based on the assumption that the underlying processes are linear and static and are apt to interpret the normal changes in operating conditions as faults, which would result in high false positive rates. On the other hand, the development of robust diagnostic techniques for the detection of incipient faults remains a challenge for researchers, given the difficulty of finding an appropriate trade-off between a low false positive ratio and early detection of emerging faults. To address these issues, this paper proposes a novel adaptive fault detection approach based on the canonical residuals (CR) induced by the combination of canonical variate analysis (CVA) and matrix perturbation theory for the monitoring of dynamic processes where variations in operating conditions are incurred. The canonical residuals are calculated based upon the distinctions between past and future measurements and are able to effectively detect emerging faults while still maintaining a low false positive rate. The effectiveness of the developed diagnostic model for the detection of abnormalities in industrial processes was demonstrated for slow involving faults in case studies of two operational industrial high-pressure pumps. In comparison with the variable-based and canonical correlation-based statistical monitoring approaches, the proposed canonical residuals-adaptive canonical variate analysis (CR-ACVA) fault detection method has demonstrated its superiorities by the detailed performance comparisons.