The invention discloses a lake-reservoir algal bloom generating mechanism time varying model optimization and prediction method based on a taboo searching algorithm and a genetic algorithm. The method comprises the steps that first, a water bloom generating mechanism time varying model is established; second, an influence factor function model base is established; third, based on the genetic algorithm, water bloom generating mechanism time varying model parameters are optimized; fourth, based on the taboo searching algorithm, a water bloom generating mechanism time varying model structure is optimized, and influence factors are analyzed; and fifth, optimum water bloom generating mechanism time varying model prediction is carried out. According to the method, a time variable is introduced into the water bloom generating mechanism model, the water bloom generating mechanism time varying model is established, so that the method is suitable for simulating a water bloom generating process and can be used for water bloom prediction, and the problem that water bloom prediction based on a data driving model is not accurate enough, and a mechanism driving model cannot predict water bloom is solved.