Soft sensing can solve the problem of on-line measuring for some variables which are difficult to measure with common instruments commendably. Chlorophyll-a is an important index of water quality for seawater, which can indicate the state of algae reproduction, further more it can predict the disaster of red tide by prediction model. The content of chlorophyll-a of seawater is affected by many physical-chemical factors, this complex relationship among them is difficult to be described by ordinary mechanism expression. In this paper, we use Fuzzy BP model to describe this complex nonlinear system, and detect the content of chlorophyll-a by the method of soft sensing. The PCA(Principal Component Analysis) method had been used to reduce the dimension of the sample data, simplify the complexity of the model system, this method can make the model has a faster convergence rate and a relative low dimension. The experiment illustrates that the result of soft sensing for algae blooms can match the real changes of the content of chlorophyll-a in seawater basically.