It’s tempting when fly fishing to consider the river or lake as a flat plane, in other words to to concern yourself with aiming your fly at objects and areas of water you can see. This is fine for dry fly fishing but for sub-surface fishing is it equally important is to try and visualise what your fly is doing under the water and how deep in the water column it is fishing. Much of the food that trout consume is beneath the surface and it can be right on the bottom, you need to be sure that your fly is getting down this far! This can be the difference between catching and blanking.
For still waters, sinking lines can help get the fly down to the required depth. Most sinking lines have a sinking rate of inches per second written on the box, this allows you to countdown the line giving you an educated guess of how deep the fly line is.
For rivers, weighted beaded nymphs can help and on slower flows these will fish nice and deep. For faster streams, beaded nymphs may only fish a foot or so deep on short nymphing runs so fishing a very heavy nymph Czech style will be a better alternative. You can also add a few split shot to the leader and fish with a standard weighted pattern – I have found this particularly effective on the Derwent here in the Derbyshire Peak District.