When you have a heavy soil that remains wet for extended periods, it affects root health dramatically. Fine, all-important roots begin to die very quickly after being exposed to saturated soil. They cannot regenerate until air returns to the soil, and then the regeneration creates a substantial energy drain on the plant, or it can kill it outright.

I would strongly advise you to repot, removing all of the old soil from the root mass and situate the tree in a free draining, well-aerated soil.

The "drainage layer" of rocks you have provided does not improve drainage, it simply raises the level of saturation in the pot as water "perches" in the soil above the rocks.

The link I'm leaving for you explains pretty much all you need to know to be able to determine an appropriate soil choice.

Al

Here is a link that might be useful: Container Soils - Water Movement & Retention

Citrus trees do not like a lot of water so make sure you're not using potting soil with moisture control. Hold off on the fertilizer until you see some growth. If the roots are stressed, they can't take up the fertilizer.

Regina

I agree that an orange tree with its feet in the water will not be happy. Repot it for sure. This may even encourage it to set flowers. However, it's not unusual to wait 2-3 years before you get any fruit.

Thanks everyone!!! I repotted it, hopefully I did not kill him in the process.