Stressors endanger lake ecosystem biodiversity and networks, especially in sandy lakes of arid/semiarid regions, where impacts are poorly understood. Here, we investigate the changes in multitrophic biodiversity and ecological networks under increasing stress (temperature, nutrients, lake area) by using sedimentary DNA from a shrinking sandy lake in China over nearly 100 years. With increasing stress, species richness and stability increased, whereas species turnover decreased. Species synchronism decreased at high-trophic levels but increased at low-trophic levels. Empirical dynamic modeling showed network connectance and strength of species interactions decreased–increased–decreased over time, signaling a potential adaption–resistance–degradation change in ecosystem responses with increasing stress. Models also indicated network structure primarily depended on direct effects of nutrients and temperature under low/medium stress and on a diversity-mediated pathway under high stress. Thus, maintaining ecological network structure complexity and integrity in lake ecosystems is essential to mitigate the effects of multiple stresses.