Species diversity and functional diversity indices reflect the variations of community structure and their responses to environmental stress. This study clarifies the biodiversity of macroinvertebrates in the Jingui River of Shenzhen and their response to the aquatic environment across different seasons. Utilizing ten functional traits, we conducted a seasonal survey at ten sampling points to examine changes in macroinvertebrate species and functional diversity, along with their relationships with environmental variables in the JGR. The results of the study demonstrated that the species and functional diversity of macroinvertebrates were significantly affected by season. Redundancy analysis indicated that water velocity, hydrogen ion concentration, turbidity, water depth, and total nitrogen were the most important factors for macroinvertebrate functional diversity. Moreover, structural equation modeling demonstrated that seasonal variations in total nitrogen, ammonia nitrogen, nitrate nitrogen, conductivity, water velocity, and hydrogen ion concentration directly or indirectly impacted the species diversity and functional diversity of macroinvertebrates. This study provides valuable information into the seasonal variation characteristics of macroinvertebrate communities, contributing to a more comprehensive understanding of biodiversity crucial for maintaining river ecosystem functioning and stability.