Toilet with brown sediment in the toilet bowl
If on a well: While it's odd to have it only at one toilet, it otherwise sounds exactly like &quot;clear water iron&quot; (dissolved iron in the water, turns to rust when the water is exposed to oxygen.) That will pass right through a filter unless it's oxygenated first.
Try filling a clean white bucket with clean water, and then wait (or stir and wait.)
Or, check your water test results for iron and manganese.
If not on a well, check your aerator screens in the downstairs faucets, particularly.
You may be getting sediment or rust from the water distribution system, in which case a whole house filter should clean that up. You may not see it upstairs yet because it may be settling out more in the lower pipes.
Try filling your clean white bucket from the lowest drain valve or hose bibb in the house, or from the lowest sink with aerator removed. You probably won't have to wait long for it to settle out if this is debris, rather than clear water iron.