The cycle of biogenic elements in lakes is intimately linked with particulate organic matter (POM), which plays a critical role in ecosystem restoration and the control of eutrophication. However, little is known regarding the functionality of ecosystem degradation on the source of POM in the water of a karst lake. To fill this knowledge gap, herein we compared the temporal and spatial distribution characteristics of POM prior to and after ecosystem degradation in the karst lake Caohai Lake, located in the southwest of China, and analyzed the source of POM using a combination of carbon and nitrogen stable isotopes (δ13C–δ15N). Our results showed that the dissolved oxygen (DO) concentration and pH values decreased, and the concentrations of POM in water increased by 11% and 31% in the wet and dry seasons, respectively. The decrease in the δ13C value of POM was accompanied by the increase in the δ15N value of POM in the water of Caohai lake. Prior to the ecosystem’s degradation, sediment resuspension (28%) and submerged macrophytes (33%) were the dominant sources of POM in lake water. In contrast, sediment resuspension (51%) was the major source of POM after the ecosystem’s degradation. Environmental factors, including DO, turbidity, water depth, and water temperature, that are related to photosynthesis and sediment resuspension are the main factors controlling the spatiotemporal distribution of POM. The resuspension of sediment reduced the transparency of the water, limiting effective photosynthesis, impeding the survival of submerged macrophytes, and, consequently, deteriorating the ecosystem. We propose that the control of sediment resuspension is important for improving the water transparency that creates an appropriate habitat for the restoration of the submerged macrophyte community.

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