There are deep holes, some filled with a bit of water. I need to find out the depth to the bottom of the hole, not just to the top of the water. Cost isn't really an issue. Could maybe go up to $1000. How they do it with aircraft is short pulses, I'm looking for something like that.I'm a bit confused as to what you want to measure as well.
If it is the water level at some static point (in a river, a well, lake etc) just driving a pole into the bottom and putting a scale on that would be the simplest solution by far.
If you want to measure water depth, such as from a boat so you can assure you'll not run into sandbanks and such, ultrasonic solutions are the industry standard, and work pretty well in murky water as well (but not always when the floor is really muddy so the transition between murky water and dilute mud is vague).
These things are available commercially for $100-ish (for the the display system and transducer in one package), fairly reliable and not that hard to install. Range is usually limited to something like 50 meters, but then again, if you need a depth of over 50 meters you don't generally care about $10.000 more or less on equipment to secure your vessel worth millions not running aground