<p>The excessive accumulation of nutrients in rivers is a significant contributor to eutrophication, and changes in nutrient levels are impacted by a variety of causes. Because the nutrients and environmental factors are highly non-stationary, we applied the time-frequency analysis-complementary ensemble empirical mode decomposition with adaptive noise and the Hilbert-Huang spectrum to investigate the fluctuations in long-term nutrient levels&#xa0;and environmental factor dynamics from 2005 to 2019 in the Yi River.&#xa0;Principal components analysis was conducted on environmental factors, revealing three principal components, labeled F₁, F₂, and F₃. These analysis techniques isolated six intrinsic mode functions (IMFs) for each nutrient and environmental factor and showed that these IMFs generally operated at similar time scales. All the IMFs oscillated throughout the series. The residual components captured the underlying long-term trend of the original series. There were no significant differences between the nutrients and principal components in the high-frequency IMFs (IMF1-3). However, significant differences were observed among the low-frequency IMFs (IMF4-6). The time-dependent intrinsic correlation analysis revealed positive correlations at specific time intervals and scales, whereas contrasting behavior might exist at others. The time-dependent intrinsic correlation analysis showed that positive correlations could be observed at specific time intervals and scales, while contrasting behavior might exist at others. However, potential factors such as unidentified physical processes, spatial non-homogeneity, or climate forcings on hydrological processes were speculated to play a role in these variations. The significance of this research lies in providing a better understanding of the temporal dynamics of nutrients and environmental factors in rivers, which can contribute to effective management strategies for eutrophication.</p>