As essential primary producers in freshwater ecosystems, phytoplankton offers insights into aquatic ecology due to its short growth cycles and sensitivity to environmental changes. However, previous publications paid most attention to phytoplankton in large water bodies (e.g., rivers, lakes and reservoirs). Limited attention was paid to smaller water bodies. This study selected a typical agricultural pond within a lowland polder in Lake Taihu Basin, and conducted one-year measurement (2022) including phytoplankton, meteorological, hydrological and nutrient conditions. Based on the measured dataset, the season pattern of phytoplankton dynamics was analyzed. A structural equation model was developed to explore the cause-effect relationship between phytoplankton and environmental factors. The relationship in the unique agriculture pond was compared with that in other large water bodies. Our investigation revealed that a total of 73 species from 55 genera and 7 phyla of phytoplankton were detected in the studied pond, with the dominant phylum of Euglenophyta. The dominant phylum in the studied pond was different from that (Cyanophyta and Chlorophyta) in large water bodies. Phytoplankton species were categorized into 22 functional groups, with 4 dominant groups of P, J, W1, W2, and an Q index of 0.63-2.38. These results revealed the characteristics of eutrophication, turbidity, and strong water mixing within the pond, and were generally consistent with water quality monitoring results (belonging to class V, with an annual average of TP=0.16 mg/L and TN=1.73 mg/L). Temperature was found to be a critical factor influencing the diversity of phytoplankton communities, while water depth was identified as a crucial factor affecting changes in phytoplankton functional groups. These driving factors was distinct from that (e.g., light and nutrient conditions) in larger water bodies. This study enhanced our understanding of phytoplankton dynamics in typical agricultural ponds within the lowland areas, and provided fundamental support to improve ecological health of small water bodies in lowland agricultural areas.