Abstract: Heishazhou waterway is a typical goose-head pattern braided channel in the lower reaches of Yangtze River. A series of engineering measures were taken in 2007 to protect critical area of the Heishazhou sand bar, including the head of sandbank, left channel and sandbank of South waterway. These measures preliminarily help stabilize the sandbank-groove pattern and improve the channel capacity. Due to the low elevation of channel bar in South waterway and weak fluid constraints of the sandbank, navigation could easily get impeded during flood years. Using mathematical model, water flow variations were calculated under three working conditions including heightened crest line, river bank failure and blocked left channel, and the results were then compared with water flow in natural state. Major reasons for navigation obstruction were found out and countermeasures were put forward, which provide reference for design of second-stage engineering scheme.