I second the "check the grounds" comment.
In fact, do more than check them, beef them up!
It is easy to create a "ground" problem when the head unit is operated off of the boat's main electrical system and the amps are wired directly to the battery. The amplifier's job is to take a tiny signal comming from the head and turn it into a large signal. The problem is that the amplifier references everything to what it considers to be "ground", which is usually a very close approximation of what is on the battery due to some really beefy cables connecting it to the battery.
The head unit, on the other hand, generally picks up its version of "ground" from up under the dash, after is has run half way around the boat, through the engine compartment, through the cable harness that connects the engine to the dash, and then a distribution panel. Any surge of current (like a pulse from the depth sounder) will create a slight shift in the "ground" voltage due to the voltage drop in the wiring. The amplifier seens this and can't distinguish it from signal.
The solution is to make a direct ground connection between the head unit and the amplifier. If you can get up behind the head unit then there is usually a good spot to connect a ground to, often doubling as a rear mount to hold the back of the head unit up. Use something like #12 or #14 wire and then run it to the Negative terminal of the amplifier.