The hole I dug filled in with water instantly...

Hey guys I dug the hole for the first plant today and i dug it out 3" by 3" by 3". The bottom 6 inches of the hole immediately filled with water because its very close to a river. I still put the potting soil in to the hole regardless. I'm just wondering basically how this will affect the plant? Will it get root rot?

I would dig around and make sure there is plenty drainage around most of the roots.
Maybe build the soil up into a mound.
raised Bed.
5 Gal bucket with the bottom Cut out. the roots will grow down into the hole, but not all will stay soaked.

I think that the plant would probably be fine right in the dirt unless the entire hole is soaked (giggity), the roots will regulate themselves. If they can't go deeper due to moisture, they'll go wider. But if you want to be extra safe, go with the 5gal bucket idea.

add a nice layer of sand between the water and soil til you have dry sand, then plant on top of it with your mix

I have heard of a dude planting a planter box on a couple fallen logs right over a small rapid in a stream behind his house . end result was roots growing into the water and down stream like a hydro setup . Hard to say what will happen for ya .

Will it get root rot?

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yes.

Roots and soil Wick up water. if there is a permanent water source at the bottom of the hole the plant will stay wet, forever. if you fill the hole with a Hydropinic medium (IE hygroton clay...) you MIGHT be able to get away with it, but you have to water your plant 3-4 times a day for the first 2 weeks....

Easiest way out of this: Dig on higher ground. simple.

I have heard of a dude planting a planter box on a couple fallen logs right over a small rapid in a stream behind his house . end result was roots growing into the water and down stream like a hydro setup

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Many people do that. google outdoor river hydroponics... But that is a completely different thing than having nasty, stagnant water in the bottom of your hole, permanently.