LM393: Electronic Fry Counter
Instead of a narrow beam, illuminate the channel, below the waterline,
 with a flood of diffuse
light (you can use a color filter to keep stray illumination from triggering the
sensor).   Then, focus with a lens so that blockage in mid-channel
occludes the light at the sensor,  causing the sensor reading to dip.  

There are good red or IR light-emitting diodes that can replace the laser, and
inexpensive acrylic Fresnel lenses that can do the focusing.

The key, here, is that rough water can randomize the light direction,
and that loses laser beam intensity at the pickup; if the light is random
and diffuse to begin with, that effect is less important.