River algal blooms pose a global ecological and environmental problem, resulting in serious consequences for watershed ecosystems and human health. However, current research has yet to fully identify factors influencing river algal blooms or accurately predict chlorophyll-a concentration, a key indicator, at various lead-times using high-frequency data. Here, we employed Empirical Dynamic Modeling (EDM) and machine learning techniques to forecast daily chlorophyll-a concentration in the Han River of China. The Convergent Cross-Mapping (CCM) analysis revealed the causal relationships between chlorophyll-a concentration and eight variables: pH, total nitrogen, water level in the Han River, water level in the Yangtze River, water temperature, permanganate index, sunlight duration and total phosphorus in the Han River. Subsequent multivariate EDM models with three lead-times (i.e., 1-day, 5-day, and 10-day) only showed acceptable performance in model training (R2 = 0.19–0.73, MAE = 2.76–9.17 μg/L), while exhibited poor predictive performance in model testing (R2 = − 0.50–0, MAE = 9.64–13.09 μg/L). However, Gradient Boosting Machine (GBM) and Random Forest (RF) models with three lead-times exhibited robust performance in both model training (R2 ≥ 0.8, MAE < 4 μg/L) and testing (R2 > 0.6, MAE < 6 μg/L), demonstrating that machine learning models were more suitable than multivariate EDM models for reliably predicting algal blooms. Our study contributes valuable tools for predicting daily chlorophyll-a concentration. The methods presented herein hold broad applicability and offer insights into predicting the entire process of river algal blooms based on daily monitoring data.