Abstract: The Yellow River Estuary (YRE) water body is currently confronting with significant environmental challenges, including escalating pollution and decreasing biodiversity. Therefore, there is an urgent need to explore the water ecological status of the YRE and identify the key environmental impact factors. In this study, the environmental DNA technology and Palmer algae pollution index method were used to monitor and evaluate the phytoplankton diversity and community composition in the YRE, and to identify the main environmental factors affecting the phytoplankton diversity and community composition. By collecting and analyzing water samples from the mainstream and tributaries of the YRE, we found that the phytoplankton diversity in the tributaries of the YRE was significantly higher than that in the mainstream (p<0.05), and the tributaries and mainstream also differed significantly in phytoplankton community composition (p<0.05). The evaluation results based on the Palmer algae pollution index indicated that there was a higher level of eutrophication in the mainstream of the YRE. The redundancy analysis identified pH, total nitrogen, ammonia nitrogen, and total phosphorus as the principal environmental factors influencing phytoplankton diversity and community composition in the YRE, accounting for over 50% of the observed variation in community composition. The research findings offer an important basis for further investigation into the current status of the water ecology of the YRE and its environmental impact factors.