Recently, maintaining a complex mechanical system at the appropriate times is considered a significant task for reliability engineers and researchers. Moreover, the development of advanced mechanical systems and the dynamics of the operating environments raises the complexity of a system’s degradation behaviour. In this aspect, an efficient maintenance policy is of great importance, and a better modelling of the operating system’s degradation is essential. In this study, the non-monotonic degradation of a centrifugal pump system operating in the dynamic environment is considered and modelled using variance gamma stochastic process. The covariates are introduced to present the dynamic environmental effects and are modelled using a finite state Markov chain. The degradation of the system in the presence of covariates is modelled and prognostic results are analysed. Two machine learning algorithms k-nearest-neighbour (KNN) and neural network (NN) are applied to identify the various characteristics of degradation and the environmental conditions. A predefined degradation threshold is assigned and used to propose a prognostic result for each classification state. It was observed that this methodology shows promising prognostic results.