The water level in the bowl of our toilet has slowly and steadily gotten lower over the last year or so. I replaced the flapper last year, could changing anything in the tank affect this? Or would that be looking at the wrong end, and I need to replace the wax seal? Any ideas on what would cause this?
The only possible reason for the water loss, and that if you're not getting any noticeable leakage, is improper venting, as described here.
There is another reason why it seems that improper venting is the cause - you noticed that the water level was getting lower over a year period. It could be that over that year your plumbing venting clogged slowly & steadily.
Also, contrary to what is said in the link above (that in a case of improper venting you need to call a plumber), I think that if you've noticed the change over a long period, this is also reversible (bird nesting or something similar).
If the problem was very low but steady water level, then it could be a problem that require a plumber's work.
I think Asaf nailed it with the vent. Here's why I doubt it's anywhere else:
Flapper: if this was leaking, you would likely see more water, not less. And if it was mis-adjusted, the problem would likely be an insufficient flush, rather than a low water level.
Supply line that runs into the overflow tube: if this stopped working, it would likely be a quick change. Though it wouldn't hurt to check this since it would be a quick fix.
Wax seal: when this goes, you'll smell it, but the water level shouldn't change.
The reason the vent seems to be the most likely reason is because when the vent doesn't allow the pressure to equalize, the water going down the drain creates a suction that pulls water out of the traps, and the toilet is just a big open trap. The same thing will happen in high winds, I'll see water in the toilets going up and down after a strong gust.