Please check out [url=http://www.phy.ntnu.edu.tw/ntnujava/index.php?topic=700.msg2526#msg2526]Pendulum with damping[/url]
The applet assume the damping force is proportional to velocity of the pendulum, which is a good approximation for object moving in water. The applet also assume the mass is always under the water. You can adjust different value for b and find the best one to fit with experimental data. (Because the real damping force also depend on the geometry/area of the pendulum).