We present a new modeling method for use in large-scale physical systems, such as the Everglades ecosystem. The current work that has been done in the ATLSS (Across-Trophic-Level System Simulation) project---which focuses on simulating key Everglades system components---relies on code integration. While this represents a necessary first step in analyzing the dynamics of species within the Everglades, it falls short of true model integration. We have constructed a methodology called object-oriented physical modeling (OOPM), which allows a comprehensive knowledge representation to be constructed for large scale systems. OOPM enforces the idea that an implementation of computer code can be accomplished in an incremental fashion by starting with a conceptual model and progressing to more detailed models. During this evolutionary procedure, a minimal amount of code is written since the emphasis is on developing the conceptual model so that it not only represents the intuitive aspects of the model, but that it is also executable. OOPM provides a kind of ``blueprint'' for ecologists, biologists and hydrologists to communicate and integrate models effectively.