The scene is one fairly near to the beginning of the film when the boat encounters some bandits firing at them from a small islet in the middle of the "river". In reality the river is Three Fathoms Cove and the small islet is the very distinctively triple hat-shaped Sam Pui Chau at the northern end of the cove. We have seen it on this blog quite recently because Madonna and Sean Penn filmed scenes nearby for Shanghai Surprise (scroll down to the third screen grab on that page and you can see the islet on the left hand side).
Here is what it looks like in The Sand Pebbles.
The screen grabs quite clearly show the three bumps (or "cups" as the Cantonese name suggests) that give Sam Pui Chau its name. The the lowest picture you can see an island in the background. This is Ma Shi Chau near Plover Cove.