The tilting of the antenna does not affect the shape of the Fresnel zone.
It does however, make sense that the lake dropping level can affect the signal strength.
What the guy was referring to when he said to tilt the antennas upward was to change how much signal hit the lake. This can be a difficult concept to talk about over text, but I'll try. It sounds like you understand what I'm about to say, but I'll elaborate for our other viewers. Let's start with some rules.
- The Fresnel zone only changes with distance and frequency. The antenna shape, type, direction, polarity, and beam width properties do not effect the FZ.
- What does change with the antenna type and mounting is the beam width and how the beam width of the antenna is effected by the environment.
One problem that I have seen is that many people use too low gain of an antenna when a high gain makes more sense. In your case, a 15dBi antenna is plenty for a 3 mile shot. On the surface it makes sense to go with a pair of 15dBi antennas.
What that doesn't take into account though is reflections. 15dBi is a great antenna, but it does have a decent size beam width. In a situation where there could be lots of reflections, such as a city center with high rise buildings, or, over a like like your situation, a good solution is to install a higher gain antenna than you actually need. If you were to install a 24dBi dish or grid antenna on each end the beam width may be so tight that there won't be reflections off of the lake.
If a 24dBi antenna is too much power, then reduce the power on the bridge to stay within a reasonable signal strength.
I've got to go to dinner (and that can't wait). Hopefully that helps a bit.