To ensure the sustainability of the marine environment, it is crucial to understand the intricate relationship between environmental factors and marine biota. Human activities have been recognized as significant contributors to profound changes in marine ecology. However, these observable alterations often represent a cumulative effect that intertwines with less apparent natural influences. This research delved into the relationships between environmental factors and marine life in the waters adjacent to Nanwan Bay, Kenting, Taiwan. Specifically, it examined the linear relationships and the degree of changes between environmental factors and marine life. To achieve these objectives, factor analysis was employed to uncover potential latent variables that could impact marine organisms, with these variables named based on previous studies and related literature. The findings led to the development of a structural equation model (SEM) to represent the marine ecology of Nanwan Bay. The results accentuated the significant influence of primary productivity and nutrient levels on the assemblage of marine life. The application of SEM methodology sheds more light on the degree of impact natural and anthropogenic interference have on marine ecosystems.