The high-performance computing systems include a large number of hardware and software components that can cause failures. Nowadays, the well-known approaches to monitoring and ensuring the fault tolerance of the high-performance computing systems do not allow to fully implement its integrated solution. The aim of this paper is to develop methods and tools for identifying abnormal situations during large-scale computational experiments in high-performance computing environments, localizing these malfunctions, automatically troubleshooting if this is possible, and automatically reconfiguring the computing environment otherwise. The proposed approach is based on the idea of integrating monitoring systems, used in different nodes of the environment, into a unified meta-monitoring system. The use of the proposed approach minimizes the time to perform diagnostics and troubleshooting through the use of parallel operations. It also improves the resiliency of the computing environment processes by preventive measures to diagnose and troubleshoot of failures. These advantages lead to increasing the reliability and efficiency of the environment functioning. The novelty of the proposed approach is underlined by the following elements: mechanisms of the decentralized collection, storage, and processing of monitoring data; a new technique of decision-making in reconfiguring the environment; the supporting the provision of fault tolerance and reliability not only for software and hardware, but also for environment management systems.