To investigate the seasonal dynamics of ecological health and the underlying microbial mechanisms in shallow lakes within irrigated areas of arid regions, this study selected Mingcui Lake in Yinchuan as the study site. Water samples were collected in spring, summer, autumn, and winter. Physicochemical water quality parameters were measured and metagenomic data were obtained. A Microbial Integrity Index (M-IBI) evaluation method suitable for seasonal comparisons was developed, and its correlations with the Water Quality Index (WQI) and functional genes involved in carbon, nitrogen, phosphorus, and sulfur cycles were analyzed. By integrating the WQI with on-site habitat conditions, reference and impaired sites were identified. After indicator screening, five core indicators were selected, and an evaluation system capable of effectively distinguishing ecosystem health status across the four seasons was established. The results showed that the health rating was predominantly suboptimal in summer, followed by autumn, while spring and winter were relatively poorer, with spring being slightly worse than winter. Spatially, the large open-water areas and reed wetlands exhibited higher health ratings, whereas the lotus pond and the inflow point consistently showed poorer ratings. The WQI and M-IBI exhibited a significant positive correlation in winter and a negative correlation in summer, indicating their complementary nature. Functional gene association analysis validated the scientific robustness of the M-IBI at the molecular level. The M-IBI developed in this study provides a methodological reference and practical basis for assessing the ecological health of lakes in the northwestern Yellow River irrigation area.