The Diannong River, a valuable river and lake resource of the northern Ningxia Yellow River Irrigation Area, plays an instrumental role in regional flood control, drought resistance, climate regulation, and biodiversity conservation. Phytoplankton and zooplankton, as crucial elements of the aquatic ecosystem, have their distribution patterns evaluated and potential influencing factors identified, thereby enhancing the understanding of community distribution patterns. Nested structures and interspecies interaction relationships bear significant implications for community distribution patterns, functions, and stability. The upstream section of the Diannong River in Yinchuan City was chosen as the study object. Water samples were collected in January, April, July, and October 2021, and the community composition of phytoplankton and zooplankton was analyzed using relative abundance, density, and biomass. The distribution matrix temperature and bipartite network methodologies were deployed to investigate their nested pattern and interaction network seasonal characteristics. The findings indicate that the water environment of the Diannong River’s upstream section displays pronounced spatiotemporal heterogeneity, characterized by weak alkalinity and high fluoride content. The plankton community composition and relative abundance showed marked differences among the distinct sampling periods. The temperature of the random distribution matrix shows a significant difference compared to the zero-sum model, revealing a notable nested pattern in plankton in the Diannong River’s upstream section. The bipartite network suggests that the plankton composition was the simplest in January and the most complex in July, with the fiercest species competition observed in January and the lowest levels of species specificity, vulnerability, and generality. Water temperature (WT), dissolved oxygen (DO), total phosphorus (TP), available phosphorus (AP), CODCr, F−, and Cl− constitute the environmental parameters influencing the overall structure of the phytoplankton community in the Diannong River’s upstream section, whereas zooplankton did not present a significant correlation with water environmental factors.