Your pond has pond sludge. I’m pretty confident on this point; it’s just the nature of ponds to have their share of the black crud at the bottom. This sludge is made up of various organic materials that end up at the bottom of your pond mixed with some of the various inorganics. It’s most likely mostly made up of bits of various plants that either start in or fall into your pond, along with dead and dying algae, bacteria, dirt, etc. The precise makeup of your sludge depends greatly on what’s in and around your pond, of course. My pond, for instance, tends to have tons of acorns from the overhanging oak trees that make their way through my net and sink to the bottom, get caught up in the sludge, and start to rot by the time I clean out the sludge in Spring (the nuts rot first, so I mostly just find capules in the sludge most years [acorn tops are called capules, by the way. I had to look that up.]).
Your pond has pond sludge, and this might not be a problem. A little bit of sludge is inevitable, but if you your pond has too much it can get to be a big problem fast. The problem is that this sludge tends to be mostly impenetrable to oxygen, depending on how thick it is. The lack of oxygen inside of it means that anaerobic bacteria reign, and their metabolisms produce hydrogen sulfide. Hydrogen sulfide is the stuff that makes that rotten egg smell when you stir up your pond bottom too much or clean out your filter after leaving it too long. It’s toxic to the other living things in your pond, which means that too much pond sludge can start to kill off other things, starting with your beneficial aerobic bacteria and algae, which means more dead things that are making up the sludge (and less aerobic bacteria working to eat the sludge from the outside), which means more hydrogen sulfide, which kills more things, even, in bad enough amounts, your plants and fish. The sludge also tends to form an oxygen-sealing layer along the bottom of your pond, which can smother and kill the slimy layer of healthy algae on the bottom of your pond, leading to even more problems.
As you can probably see, this can turn into a runaway problem, especially in smaller ponds with more delicately balanced ecosystems.
So, how do I control the sludge?
The first step is preventing the sludge from building up too much. You can do this in three ways: physical, biological, and chemical. The physical route means keeping sludge-forming debris out of your pond. Few things do more for this than a good pond net over your pond in fall and winter. You should also take care to keep things like grass trimmings from straying into your water, as well as making sure that fertilizers and other lawn chemicals don’t find their way in. You’ll also want to trim back and remove dead and dying plants in your pond to keep them from falling to the bottom and rotting. Keeping stones on the dirt of your pond plants to keep your fish from digging them up can go a long way, too.
The biological route means keeping your pond stocked with healthy aerobic bacteria, be it in a biological filtration system or just loose in the water. You’ll also want to keep your slime layer of algae healthy (for instance, I don’t ever recommend power-washing the bottom of an established pond). The chemical way of preventing pond sludge is to keep the most important thing for a healthy pond flowing: oxygen. This means aeration (which, for my money, is one of the best things you can do for a pond to keep it healthy). An aerator adding oxygen to the lower levels of your pond will keep your slime layer and aerobic bacteria healthy, as well as keeping the sludge layer from forming a seal to keep out oxygen.
The second step in treating pond sludge is physically removing as much of it as you can. This can mean just reaching in there and grabbing the black crud, pulling it out, and getting rid of it. It’s not pleasant (though it is oddly satisfying), but if your sludge problem is bad enough there may be no way around it. Either way, you’ll probably want to get and use a good pond vacuum, as your hand just isn’t a good enough tool to get rid of the sludge that’s in between rocks or loose in the pond. It’s pretty easy work, vacuuming a pond with good equipment, and you’ll be amazed at how much difference getting rid of most of your sludge and debris will make in both water health and how nice your pond looks. Keep in mind that you’re never going to get rid of all of your sludge (see above, re: “your pond has sludge”), but you can certainly keep it well under control with just a little bit of work.
Finally, if you’ve developed a sludge problem, you’ll want to add extra beneficial bacteria get your pond back on track (even after you’ve physically removed it). I’m a big fan of Biocuda Biomax bacteria additive, which has not only healthy bacteria cultures but also activated barley in one additive.