The knot, the rope material, movement, and water all make a difference. I wonder if some of your problem isn’t movement over time, rather than just the water.
Several excellent knots became less effective with the transition from natural rope fiber to synthetic.
For example, the bowline is a workhorse knot, but with synthetic rope I prefer the water bowline:
http://www.geocities.com/roo_two/waterbowline.html
Other times it can be as simple as adding a half hitch or two with the loose end.
Or you could try using different rope
For each application there are a variety of knots to choose from – there is no simple, single answer.
Following is a suggested knot to try in each of the classic categories:
Binding knot (e.g. to tie a package): constrictor (on the website you referenced, under boating)
Bend (to join two lines): figure eight bend (on the website you mentioned, under climbing)
Loop: water bowline, mentioned above.
Hitch: (to join a line to an object): anchor bend (on the website you referenced, under boating)
Another favorite is the vibration-proof hitch. Unfortunately, I haven’t found it on the web, only in Maria Costantino’s
handbook of knots.