Vegetation phenology is considered an essential biological indicator in understanding the behavior of ecosystems and how they respond to environmental cues. However, the potential of interannual variations of remotely sensed phenology signals to differentiate plant types remains poorly understood, especially in understudied systems with highly heterogeneous landscapes such as wetlands. This study presents a case study in a San Francisco Bay area marsh that investigates the usefulness of interannual variation, defined as the root-mean-square error of enhanced vegetation index (EVI) measurements against a fitted phenology curve, at the beginning, middle, and end of the growing season as indicators of plant types. The study found that altitude above sea level and certain land surface phenology metrics, such as the day-of-the-year of the end of the season, the mid-autumn day, and the greening rate before the summer peak, were significantly related to these interannual variation trends. These results indicate that a detailed time-series analysis at the beginning and end of growing seasons may enhance large-scale wetland characterization. Overall, the findings of this study contribute to our understanding of vegetation phenology and provide a framework for more accurate wetland classification in future studies.