Human activities are altering global biogeochemical cycles of nitrogen (N), phosphorus (P) and biogenic silica (BSi). In order to reveal nutrient dynamics in response to human disturbances, this study explores burial rates and ratios of N, P and BSi in 210Pb-dated sediment cores from eight lakes in the middle Yangtze River floodplain. Mean burial rates of N, P and BSi increased substantially from the early 20th century, except for a hiatus in the 1970s. Before the 1960s, the stable ratios of N:P, N:BSi and P:BSi indicated the nutrient supply from clastic sources, while arable land expansion enhanced nutrient burial in lakes. Although damming increased the retention of N, P and BSi in upstream reservoirs after the 1960s, anthropogenic N and P release to the lakes outpaced the retention by dams, as suggested by continuous increases in N and P burial rates. The concurrent increase in BSi burial rate suggested that nutrient enrichment promoted diatom production at the earlier stage, while rising N:BSi and P:BSi ratios and declining BSi burial rate from the 1990s indicated the Si depletion with further eutrophication. Spatial heterogeneities among the lakes were linked to site-specific factors such as hydrological connectivity and macrophyte growth. Synchronous increases in N, P and BSi burial rates before the 1960s mainly responded to deforestation and arable land expansion; thereafter, the decoupling of N, P and BSi likely resulted from intensive farming (e.g., fertilizer usage) and damming. Given new dam construction and land use change in river basins, the BSi depletion relative to N and P is likely occurring in riverine floodplains worldwide.