Unfortunately most commercial farms aren’t putting in what they’re taking out, even with the industrial fertilizers. Most of the industrial fertilizers are just nitrogen, potassium, and phosphates, often as a liquid. You are absolutely right that you can’t take and never return; that’s why in pre-industrial revolution times, people would rotate fields between crops, and lying fallow/being used for grazing (where sheep, cattle, etc. were leaving free fertilizer) You also ended up with fewer years where all your crops got wiped out by a single pest, because you weren’t farming just one thing. Efficiency in farming–esp. monoculture–is great for profits, not so great for the land itself.

Good news is that good water treatment plants will pull phosphate out of the waste water.

Eh. High levels of phosphates end up running off fields into waterways, and then you get things like algae blooms. Waste water treatment plants will clean up runoff that goes into the sewers and storm drains, but it’s not really cleaning up entire rivers. IIRC, that used to be a much more significant problem; I remember water in rivers near where I grew up–which was all surrounded by farms–often had white, sludgy scum anywhere that the current was forming eddies. If I remember correctly the high levels of that white shit was due to worse regulations governing agricultural run-off.