Harmful algal blooms are a major type of marine disaster that endangers the marine ecological environment and human health. Since the algal bloom is a complex nonlinear process with time characteristics, traditional statistical methods often cannot provide good predictions. In this paper, we propose a method based on machine learning with the aim to predict the occurrence of algal blooms by environmental parameters. The features related to algal bloom growth have been experimented for achieving a good prediction of algal concentrations by a combination strategy. We validate the prediction performance on two real datasets from two locations in US and China, i.e., Scripps Pier, California and Sishili Bay, Shandong, respectively. The models and feature subsets have been selected to complete the missing data and predict the phytoplankton concentration. The results demonstrate the efficiency of our method in the short-term prediction of concentrations by selecting appropriate features. The comparison studies prove the advantage of our developed machine learning method. The importance of every features for the prediction performance reveals crucial factors for the outbreak of harmful algal blooms.