This depends upon the type of FW tank you have and if you are using undergravel filters and/or live plants.
If you have an undergravel filter it is important to vacuum the gravel and do it all the way to the filter plate. You want it clean, but not too clean, since this it your primary biological filter. With under gravel filters, you also need to flush out from under the filter plate from time to time. Some people do an almost complete tear down and set up of the tank every few years. If you don't to this cleaning you will tend to get dead spots in the filter bed, because that area is clogged with dirt.
If you don't use an under gravel filter, then you still want to vacuum but only go about 1" deep.
In planted tanks where a material such as layerite is mixed with the bottom layer of gravel, be sure you don't vacuum into that layer.
In FW tanks you don't usually have nitrate or phosphate issues, because in non planted tanks, you are using rather low light levels, so there should be little of no algae. In planted tanks, nitrate and phosphate are plant food, so as long as the levels don't get too high, the plants will consume it. It's amazing hoy much a dense planted tank can pull out.