A couple of transducer characteristics that can affect performance are transducer frequency and and the "cone" angle.
Lower frequency sound will have less attenuation (dissipation of energy) than higher frequency sound over the same distance (depth). Dual frequency transducers allow you select one frequency of two. If your transducer and multifunction display allow you to do this, selecting and using the lower frequency will provide better results at depth.
Switching to a lower transducer frequency will reduce the sensitivity and reduce the clutter. A lower frequency transducer - like 90 kHz will perform differently than say a 200 kHz transducer and improve your chances of "seeing" the bottom at 350 feet.
You didn't mention your speed. If you are travelling at planing speed (20 knots) and your transducer has a narrow "cone" angle you may be out of position to receive the return signal in deeper water. I find it hard to maintain a signal in less than 200 feet of water at 25 knots and impossible in 500 feet at 25 knots.
Turbulence, air bubbles, chop will dramatically affect performance. Where and how your transducer is mounted will affect performance. Shooting a transducer beam through a fibreglass hull, will also affect performance.
I have some work experience in commercial sonar. There is a guy on "the hull truth" forum, Semper Fi? , who is a real expert at diagnosing these issues. You may want to check those threads.
Hope this is helpful.
