I keep boxes that contain lures that are not rusty. Once I use a lure, it always goes in another box away from my non rusty lures. I try to keep each used lure in its own section of the rusty box as well. Every so often, I inspect my rusty box and remove and replace any rusty hooks and transfer the non rusty lures to the non rusty box.
I use this same procedure for hooks as well.
This works for me even in salt water. However, in salt water, I just toss hooks at the end of the day or trip. And I often use small plastic bags for lures.