Depending upon the circumstances of
course, most ponds naturally fill in over time. Even small creeks have this happen. A friend in NY with a creek running through his pasture cleans out the creek bottom every few years. Of course the government doesn't want people to do this anymore, but without clearing the bed out, the creek would naturally silt in and create a bog in the middle of the pasture. This creek is home to plenty of fish and other
water wildlife which would cease to be if the creek silts over. I don't know what he does with the dredgings.
I have two small ponds on my farm which accumulate a few inches of muck on the bottom each year. I regularly harvest the muddy muck to add to my garden beds. Rather than leave it pile up yo become a Herculean chore every 5-10 years, I frequently dip a net and take out a 5 gallon
bucket of muck. I see it as a resource that my farm provides for me.