Abstract Better understanding of the responses of algal biodiversity to multiple pressures, such as climate warming and eutrophication, is a key issue in aquatic ecology. Alpha and beta diversity may have various patterns over temporal scales, especially in the Anthropocene, when external pressures became more multifaceted. However, the limited availability of historical data hampers the exploration of algal biodiversity through time. Recently, sediment DNA has emerged as a potential tool for elucidating temporal patterns in algal communities. Here, we used sediment DNA to reconstruct temporal turnover and diversity of algal communities in four remote lakes in northern China over the past 200 years. Furthermore, to distinguish the contributions of possible influencing environmental factors, we conducted structural equation modelling. Our results revealed that algal communities have experienced rapid shifts since the Anthropocene, characterized by increased alpha diversity and decreased temporal beta diversity. Warmer climate and eutrophication were associated with changes in alpha diversity, while temporal environmental variation was associated with temporal beta diversity. This study revealed opposing patterns in alpha and beta diversity for algal communities, possibly caused by warming, eutrophication and lower temporal environmental variation, respectively. While climatic factors played a major role in remote lakes with a natural environment, lakes that are more human impacted may be more structured by nutrient‐related factors. Under climate warming and intensified human activities, remote lakes may encounter complex pressures in the near future. Our findings offer valuable insights into patterns in aquatic biodiversity and possible factors underlying multiple pressures.