You've got a number of options:
1) Place the bottle emptier very close to your terrariums, and set its priority a bit higher. Make sure to enable auto-bottling on the emptier, as well. If your dupes still aren't emptying the bottles, they have too much to do and you need to further tune your priorities. If space is at a premium around your terrariums, you might need to empty the bottles into a small reservoir with a pump to get rid of the water.
2) Leave the bottles alone and put down some Deodorizers. PH2O offgases PO2, which the deodorizers will clean. It doesn't take all that many cycles for the offgassing to provide more O2 than the terrariums (I haven't played since shortly before release so this may have been tuned).
3) Use a mod like this one to add a piped output to your terrariums, so you can pipe the PH20 directly to a sewer or sieve.