The information of instream biotype, i.e., types, location, distribution, etc, are important for estuary environment management. Field observations carry out by ecology surveyor is the standard procedure to gather that information, which is time consuming and difficult to be applied to a large spatial extend. In this research, we propose using airborne for instream biotype classification. Texture of point clouds is the key to distinguish between flow types, and semi-variogram was employed for texture measurement of different flow types. The principle component analysis is then used for classification and data compression. The results show that the first principle components are closely related to the flow types considered in this study.