The Weihe River Basin plays an indispensable role in the water environment and water ecological balance in Northwest China and the lower reaches of the Yellow River. In the context of river ecosystems being affected by climate change and human activities, phytoplankton, as primary producers in food webs, serve as an important ecological indicator of environmental change. As such, systematic surveys on the water environment and phytoplankton were carried out in the Weihe River mainstem and its five tributaries from the northern foot of the Qinling Mountains from October to November 2017 and April to May 2018. In total, 154 species of phytoplankton belonging to 69 genera were identified in the heavy sediment-laden mainstem, with an average density and biomass of 177.57*10 cell L and 6.53 mg L, respectively. Furthermore, a total of 207 species of phytoplankton belonging to 81 genera were identified in the five tributaries originating in the Qinling Mountains, with an average density and biomass of 80.98*10 cell L and 1.90 mg L, respectively. Canonical correspondence analysis (CCA) was employed to analyze the relationship between phytoplankton communities and environmental factors. The results of data screening and Monte Carlo sequencing tests revealed that water temperature (WT), dissolved oxygen (DO), and nitrite nitrogen (NO-N) were the primary environmental factors affecting the distribution and abundance of phytoplankton in the Weihe River mainstem. WT, flow velocity (V), pH, conductivity (Cond), and NO-N predominantly structured the phytoplankton communities in the Weihe River tributaries. The results of this study are useful for the ecological management and conservation of the mainstem and tributaries of the Weihe River Basin.