How can I know where wind is coming from by looking at water?
The easiest way to tell the direction of the wind when you're near the water is to look for something on the shore that indicated wind direction (beaches often have flags on them)

Barring that there are a bunch of other clues that should be familiar to any sailor (or seaplane pilot) which you can borrow:


Boats lying at anchor weathervane and automatically point into the wind
This isn't 100% reliable: Some boats will set two anchors (fore and stern) and won't weathervane. Also when the tide is shifting boats will swing to align with the tide if it's stronger than the wind. 
Boats lying at anchor sometimes have a flag on them
Flags on a boat at anchor work the same way as flags on land - they're excellent indicators of wind direction.
On calm bodies of water the wind creates visible surface ripples
The concave side of these ripples is the windward side.

(Visualize the water as being a large bowl of soup - now blow on the soup. The ripples will have the same shape.)
This same principle applies to larger waves as well (other factors could cause the dominant breeze along a shoreline to not be quite perpendicular to the waves, but if your concern is ground reference maneuvers it's "close enough").
"Wind Streaks" on the sea indicate wind direction
Wind streaks are somewhat ambiguous in that they're aligned with the wind, but don't tell you which way it's blowing: You have to figure that out for yourself (for example by looking at the shape of the waves as described above).

Surf spray gives wind speed and direction
Waves breaking will produce spray that blows downwind - I couldn't find a good illustration for this, but the finer spray tends to blow, while heavier drops just fall. The distance the spray blows gives an approximate indication of wind speed.
It would take some pretty heavy seas to produce visible spray at altitude though, and you're more likely to see foam and whitecaps in that case
Foam or Whitecaps provide wind speed and direction
Foam or whitecaps provide an indication of direction (the foam appears to move upwind - into the wind) and speed (it generally takes winds of 10-15 knots or more to produce whitecaps and foam).