The community structure of protists reflects the environmental conditions during the period when the living environment was sampled. Biodiversity index, species composition and abundance can reflect various changes in the environment, indicating the quality of water quality during this period. Protists are ideal target species for environmental monitoring and can be used as indicator organisms. However, due to the few morphological characteristics of protists, they are easily affected by environmental pollutants and change their own form. The manual monitoring method has the possibility of human error, and long-term monitoring requires a lot of time and energy. The work caused great difficulties. Therefore, a monitoring technology that can efficiently monitor the protist community has important application value for environmental monitoring and biodiversity conservation. The digital holographic microscopic imaging technology has the characteristics of three-dimensional imaging, and can observe the community structure of protists. In this paper, this technology is used to monitor the community of protists in the sediments of the lake and river basins. Quantitative sequencing technology was used to analyze the diversity of protists, and the calculated alpha diversity index of the protist community was used to reflect the quality of water quality.