The advancement of complex biochemical modeling has been greatly aided by the standardization of machine-readable formats such as Systems Biology Markup Language (SBML) and the development of the diagrammatic Systems Biology Graphical Notation (SBGN). Leveraging these tools, the graphical SBML editor Cell Designer enables seamless translation between SBGN and SBML. However, the kinetic rate laws remain a challenging process, often demanding manual assembly and specialized knowledge of kinetic equations. In this study, naphthalene, a ubiquitous polycyclic aromatic hydrocarbon, poses environmental challenges due to its persistence and potential toxicity. Utilizing tools like Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN), formalized models capture the interplay of enzymes, intermediates, and regulatory factors. The integration of kinetic rate laws facilitates the prediction of degradation rates under varying environmental conditions. In natural environments, factors such as pH, temperature, oxygen availability, and microbial community composition influence the efficiency and rate of degradation. These tools facilitate in providing a standardized format for encoding the model which ensures interoperability with various modeling tools and provide graphical representation for enhanced visualization. Additionally, the fate of degradation by-products and the potential accumulation of toxic intermediates warrant consideration for a comprehensive assessment of environmental impact. We present a comprehensive modeling pipeline designed to yield a mathematical description of the biochemical reaction system governing naphthalene metabolism in Pseudomonas aeruginosa.