Before you change your fly, run through three questions at the end of each drift. This takes about ten seconds and will tell you more than any amount of fly box digging.
Question one: Is the fly at the right depth? If you're not ticking the bottom occasionally in slower water, you're probably too shallow. Not every cast needs to drag bottom, but if you're never near it in the right water, add weight or lengthen your indicator setting. If you're constantly snagging and can't get a clean drift, you're too deep or too heavy for that current speed.
Question two: Is the fly moving at the right speed? Watch the indicator. Is it moving faster than you'd expect the deep current to be moving? In most runs there's a visible difference between surface speed and what the deep current is doing – you can often see it in foam lines or debris on the water. If the indicator is racing, the fly is lifting and speeding up too. Mend upstream earlier and more aggressively.
Question three: Do I have enough contact? At the end of the drift, is there a large belly of slack downstream of the indicator? That slack accumulated during the drift, which means your contact was degrading throughout. Try a shorter drift with tighter line management, or reposition to reduce the angle.
Now for the harder part – understanding what different indicator behaviors actually mean:
The indicator stops and holds briefly, then moves again. This is often a bottom tick – the fly dragged into something on the substrate. Not a take. Adjust weight or shorten the drop slightly.
The indicator dips and immediately comes back. Could be a rock, could be a fish. The difference is usually how sharp and decisive the movement is. A fish take tends to be more deliberate. A rock tends to be sudden and then the indicator pops right back.
The indicator slows or draws to the side without a dip. This is one of the most commonly missed takes. The fly paused in the current – either a fish inhaled it or it moved into a slower seam. Set the hook. It costs you nothing.
The indicator moves at a steady, natural pace through the whole drift. That's what you're after. Learn what it looks like so you can recognize when something interrupts it.