Black bloom is a very serious water pollution phenomenon in eutrophic lakes, with Fe(II) and S(−II) being the key limiting factors for this problem. In this paper, three different machine learning methods, namely, Random Forest (RF), Gaussian Mixture Model (GMM), and Bayesian Network (BN), were used to explore the complex interactions among Fe(II), S(−II), and other aquatic factors in the estuary of Chaohu Lake to better characterize and monitor water degradation by black bloom. The results of RF showed that total nitrogen (TN), ammonia, total phosphorous (TP), suspended sediment concentration (SSC), and oxidation–reduction potential (ORP), which were chosen from 11 factors, had the most important relationships with Fe(II) and S(−II). The 69 sampling sites were divided in three groups identified as worst, worse, and bad according to the observed values of seven factors using the GMM. Then, the BN model was applied to three observation groups. The results showed that the structures of the interaction networks were different between the groups. S(−II) controlled only SSC production in the bad and worse group sites, while SSC was determined by both S(−II) and Fe(II) in the worst group. Ammonia and TN exhibited the most direct importance for S(−II) and Fe(II) production in all observation groups. According to the indications from the BNs, potential management strategies for different water pollution conditions were developed. Finally, the threshold values of Fe(II), S(−II), TP, ammonia, TN, SSC, and ORP, which were 0.80 mg/L, 0.04 mg/L, 0.45 mg/L, 3.44 mg/L, 4.15 mg/L, 55 mg/L, and 135 mv, respectively, were determined on the basis of the BN models. These values will be helpful to develop accurate strategies of oxygenation to quickly eliminate black bloom in the lake.