Algae terrarium: automatically empty bottles

You did (almost) everything correctly already: 1. Place terrarium which produces pWater bottles. 2. Construct bottle emptier nearby. 3. Set bottle emptier to accept polluted water 4. do not set it to sweeping only (cause then it will accept only bottles marked with 'k') 5. raise the priority of the emptier sufficiently high

Important is step 5, where you set the priority of the emptier (also important might be the distance between bottle and emptier). If your dupes have many tasks to do, you need to micromanage the priorities. You should also note that only one bottle can be emptied at the same time. So if you have 1000 bottles lying around, there will only be one transport task active at the same time (in that case you might want to add additional emptiers).

Later on you can also use an automated sweeper (conveyor tech) to empty the bottles for you.

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.