Primary producers play key roles in maintaining a clear-water phase and promoting biodiversity in shallow aquatic ecosystems. Environmental stressors from anthropogenic activities, such as eutrophication and pesticide pollution, individually and in combination, can drive these ecosystems into a turbid state, potentially leading to a regime shift. In this 111-day study, we used 40 mesocosms (200 L) to simulate shallow lakes dominated by two typical macrophytes: the bottom-dwelling densely Vallisneria denseserrulata and the floating Spirodela polyrrhiza, along with associated food web components. We tested the interactive effects of nutrient loading, glyphosate-based herbicides, and imidacloprid insecticides on the growth of aquatic plants, phytoplankton, and periphyton. Our results indicate that meso-eutrophication, glyphosate and imidacloprid directly or indirectly affected aquatic primary producers, with the type of interaction (synergistic, antagonistic and additive) related to the form of the primary producer. Meso-eutrophication alone increased the biomass of all organisms except submerged plants, glyphosate alone decreased the biomass of all organisms except phytoplankton, with particularly strong effects on aquatic plants, and imidacloprid alone affected only aquatic animals. While combinations of multiple stressors generally increased algal biomass and decreased macrophyte biomass, submerged macrophytes consistently helped control algal blooms. These results demonstrate the risk of algal blooms in shallow lakes within agricultural landscapes and emphasize the crucial role of macrophytes in preventing algal blooms and maintaining healthy lake ecosystems.