This research is concerned with causal understanding and qualitative reasoning of behavior of physical systems, which are crucial issues of model-based problem solving. In this paper, we describe a domain ontology of fluid systems and an ontology of time for generating causal ordering in terms of components. Our ontology design has been done according to the following three criteria : cognitive causal explanations in terms of components, reusability of components and disambiguation of reasoning results. We discuss in-depth requirements for domain ontologies and propose a causal specification scheme to represent component's local causal properties and an ontology of time to enable intuitive causal ordering of complex behavior originated in the combination of components. We identify causality of fluid systems following the requirements and describe reusable models of crucial components of plants and general properties of fluid and heat for deriving global knowledge. A method of qualitative reasoning and causal ordering is discussed together with its capability and mechanism. The ontologies have been successfully applied to nuclear power plant modeling and its qualitative simulation. Reasoning results matched those obtained by domain experts.