The long-term accumulation, burial and release of nutrients, such as carbon (C), nitrogen (N) and phosphorus (P) in lacustrine sediments are responsible for the global lake eutrophication. Interpretation of the spatiotemporal sedimentary record of nutrients (C, N and P) in contrasting trophic level of lakes is helpful for understanding the evolutionary process of water eutrophication. Based on the radiochronology of 210Pbex and 137Cs, a comparative study of spatial and temporal concentrations, burial of total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP), the sources of organic matter were conducted using sediment cores from two plateau lakes Dianchi (DC) and Fuxian (FX) of SW China. Results showed that concentrations and burial of C, N and P in sediments of DC, a shallow hypertrophic lake with the maximum depth of 5.8 m, were both higher than those in FX, an oligotrophic deep lake with the maximum depth of 155.0 m. For both lakes the molar ratio of TOC/TN increased in the sediments moving from north to south. The values of TOC/TN molar ratios increased over time in DC and was higher than in FX. The extremely high values of TOC/TN appeared in the central and southern parts of FX, indicating the impacts of accumulation effect and sediment focusing in the deeper region and indirect supplement from the Lake Xingyun (XY), an adjoining lake connected with FX via the Gehe River. Time-integrated sources identification in DC indicated the contribution of allochthonous sources was dominant over the past few decades, which contributed to the increased trophic level of the lake. The comparison of relationships of carbon accumulation rates (CAR), nitrogen accumulation rates (NAR) and phosphorous accumulation rates (PAR), the ratios of N/P and the utilizations of N and P fertilizer between DC and FX implied that both of N and P inputs should be limited for reducing the trophic level, but N control was predominant in comparison with P for both lakes. The results indicated that caution is required in plateau lakes to limit transition from oligotrophic to eutrophic in these lakes.