Living soil and rain water problem

Rain water should not be an issue if collected and stored properly. My guess is you are running out of nutrients in your soil and you should amend the soil to add more nutrients back in. Water enough to fully saturate the medium and always keep it moist. Drying out the soil will kill off a lot of the “living” organisms in the soil. I hope this helps.

Not an expert on living soil or rain water but regular soil outside is living and gets rained on all the time and there’s plenty microbial life everywhere outside