Rapid algal proliferation in human-impacted freshwater ecosystems necessitates advanced predictive tools for effective management. This study aims to capture the stochastic dynamics of algal blooms in the Fuxi River, China, using high-frequency monitoring and interpretable machine learning. A 2 h interval dataset was utilized to construct Random Forest models in Python for predicting Chlorophyll-a (Chl-a) and algal density, both measured via in situ multi-wavelength fluorescence. Model interpretability was achieved through SHAP (SHapley Additive exPlanations) analysis to identify non-linear environmental drivers and ecological thresholds. The models demonstrated high predictive accuracy. SHAP analysis revealed that dissolved oxygen (>10 mg/L) is the primary diagnostic indicator for peak Chl-a, with an optimal thermal window of 15–20 °C identified for proliferation. For algal density, chemical oxygen demand (COD_Cr > 25 mg/L) and conductivity (>1000 μS/cm) were identified as critical tipping points, showing pronounced synergistic effects between organic enrichment and nutrient levels. This study underscores that managing organic loading and monitoring specific thermal–hydrochemical windows are vital for mitigating extreme algal events, providing a robust, interpretable framework for real-time water quality early warning.