We have a bay laurel tree in the back garden. We have noticed the pot is no longer draining. It’s been filling up with rain water for months now. I’ve been too worried to go near it! Too much googling about legionella and n fowleri. We can’t avoid it any longer. How do we safely get the water out? The tree is long dead I’m afraid!
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Tip the pot on its side somewhere it doesn't matter that excess water will flow out, prop up the bottom on a brick or something so the pot is angled downwards at the top, and wait a day or three till all the water has drained away, then empty out the soil in the pot somewhere on soil, or dispose of it. If you are over anxious about catching something from it, wear a mask and gloves, but its likely no more risky than taking potting soil from a bag in a closed environment, another possible source of Legionnaires, along with wet leaves. Probably a bigger risk of getting a mosquito bite, since they breed in stagnant water.

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