Not sure what kind of sensors that you have, but speed over ground is true speed, as measure by a gps. Speed in relation to water can be more variable, depending on currents, etc. You could be going 5 mph on the gps, but your speed in relation to the water might only be 3mph if you are traveling with the current. Maybe 7mph if you are against it (assuming a ~ 2mph current)
Also, many times the “water wheel” speed sensors aren’t entirely accurate, so they almost always differ from gps speed by a little bit. I’d trust the gps unless you know there is a noticable current.
There is almost always some sort of current in whatever body of water you are on depending on conditions (including lakes.) Lakes currents actually can be quite comples, depending on wind speed, direction, coriolis effect, etc… Great lakes have amazing currents, a lot of guys buy speed sensors to measure actually speed at the cannonball, which takes into account current speed (with or against)