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CO2 dilemma

Perhaps someone on the APD can help with this puzzle. Lately I have had
unhappy fish in the morning due to high CO2 levels. This morning for
example all the fish were breathing heavily. They were not at the top
gasping but obviously close. I drove off some CO2 with an airstone and put
the lights on to start the plants using it up. Everything was fine and back
to normal within an hour. This has happened twice before... once so badly I
lost my 3 largest fish. The puzzle is that according to the KH/pH charts my
CO2 should not be a concern. I use a pH controller which is working fine. I
double check that the electrode is reading correctly often and it is always
accurate with a Lamotte pH test kit. KH was 4 when I measured it before
going to bed....AFTER a small water change and quite a large plant prune.
This seems to happen after a water change and plant prune even though all
parameters seem right. What is going on here? This morning pH was 6.81 and
KH 4 that should give a CO2 level about 23 (I think that's the number...
chart isn't here) which is not lethal, is it? Is there something in my
water that raises the KH that my test kit does not measure? Am I hardening
my water more than I need to? The chart shows that the high CO2 reading
come with high KH readings. Can someone tell if there are things that raise
KH but will not register with a test kit?

in Vancouver