u/KneeMost9130

Hey guys,

I'm a civil engineer by trade but I've been getting heavily into goldfish keeping lately. Naturally, my professional background kicked in and made me want to design the filter like a mini water treatment plant. I don't have any formal training in microbiology or aquaculture—everything I know comes from self-studying research papers—so I'm pretty sure I've either overengineered something or completely misunderstood the biology here.

The system has been running for about 6 months now, so it should be matured, but I keep hitting the same walls.

To give you the physical breakdown: It's a small 60x40x40cm glass tank (around 96 Liters / 25 Gallons). The flow rate is quite high, running a 1200 L/h pump which gives it roughly a 12.5x hourly turnover rate. Water gets pumped down near the bottom of a DIY PVC settling pipe (90mm OD, 1.3m tall), flows upward through spiral brushes and filter floss, exits through a mechanical filter sock, and then flows into an overhead baffled sump (80x15x15cm) packed with lava rock biomedia before returning via a DIY venturi. Because I'm heavy feeding the fish right now, I flush the sludge from the settling pipe every 2 days and do water changes twice a week. Tap water pH is around 7.5.

On the bacterial side, I’ve been dosing a specific cocktail based on what I read. I use a heterotrophic Bacillus blend (subtilis, licheniformis, polymyxa, megaterium), some generic commercial autotrophs (AOB/NOB) from a Chinese brand, and Paracoccus pantotrophus. My underlying theory with the tall settling pipe was to let a thin sludge blanket form at the bottom to act as a mild anoxic zone, hopefully triggering denitrification via B. licheniformis.

But here is where things are going wrong and I need a sanity check:

First, I have a persistent nitrite bottleneck. Ammonia is almost always at a solid 0 mg/L, but Nitrite (NO2) constantly hovers around 0.2 mg/L. It will randomly drop to near 0 for a short bit, then bounce right back up. At the 6-month mark, why are the NOB struggling so much to catch up? Is my 12.5x turnover rate simply too fast for them to colonize the media properly?

Second, my pH is crashing violently. It refuses to stay stable at 7.0, dropping rapidly from the tap's 7.5. I'm constantly adding baking soda to boost alkalinity and buffer it back up. Concurrently, my filter socks and floss clog insanely fast with a thick, yellowish-brown biofilm. I know autotrophic nitrification consumes alkalinity, but could these Bacillus heterotrophs be hyperactive, hogging the oxygen/space and compounding the pH crash? Or am I missing a different chemical reaction here?

Lastly, I'm confused about Paracoccus pantotrophus. I bought it because literature says it’s capable of Heterotrophic Nitrification-Aerobic Denitrification (HN-AD) simultaneously under aerobic conditions. However, the actual product label only claims it eliminates Hydrogen Sulfide (H2S) and mentions nothing about nitrogen. Did I fall into a strain-specific trap, or did I totally misapply this bacteria for an aquarium context?

Would love to hear some thoughts from the microbiology or wastewater crowd here. Where is my logic failing?

Thanks in advance!

Hey guys,

I'm a civil engineer by trade but I've been getting heavily into goldfish keeping lately. Naturally, my professional background kicked in and made me want to design the filter like a mini water treatment plant. I don't have any formal training in microbiology or aquaculture—everything I know comes from self-studying research papers—so I'm pretty sure I've either overengineered something or completely misunderstood the biology here.

The system has been running for about 6 months now, so it should be matured, but I keep hitting the same walls.

To give you the physical breakdown: It's a small 60x40x40cm glass tank (around 96 Liters / 25 Gallons). The flow rate is quite high, running a 1200 L/h pump which gives it roughly a 12.5x hourly turnover rate. Water gets pumped down near the bottom of a DIY PVC settling pipe (90mm OD, 1.3m tall), flows upward through spiral brushes and filter floss, exits through a mechanical filter sock, and then flows into an overhead baffled sump (80x15x15cm) packed with lava rock biomedia before returning via a DIY venturi. Because I'm heavy feeding the fish right now, I flush the sludge from the settling pipe every 2 days and do water changes twice a week. Tap water pH is around 7.5.

On the bacterial side, I’ve been dosing a specific cocktail based on what I read. I use a heterotrophic Bacillus blend (subtilis, licheniformis, polymyxa, megaterium), some generic commercial autotrophs (AOB/NOB) from a Chinese brand, and Paracoccus pantotrophus. My underlying theory with the tall settling pipe was to let a thin sludge blanket form at the bottom to act as a mild anoxic zone, hopefully triggering denitrification via B. licheniformis.

But here is where things are going wrong and I need a sanity check:

First, I have a persistent nitrite bottleneck. Ammonia is almost always at a solid 0 mg/L, but Nitrite (NO2) constantly hovers around 0.2 mg/L. It will randomly drop to near 0 for a short bit, then bounce right back up. At the 6-month mark, why are the NOB struggling so much to catch up? Is my 12.5x turnover rate simply too fast for them to colonize the media properly?

Second, my pH is crashing violently. It refuses to stay stable at 7.0, dropping rapidly from the tap's 7.5. I'm constantly adding baking soda to boost alkalinity and buffer it back up. Concurrently, my filter socks and floss clog insanely fast with a thick, yellowish-brown biofilm. I know autotrophic nitrification consumes alkalinity, but could these Bacillus heterotrophs be hyperactive, hogging the oxygen/space and compounding the pH crash? Or am I missing a different chemical reaction here?

Lastly, I'm confused about Paracoccus pantotrophus. I bought it because literature says it’s capable of Heterotrophic Nitrification-Aerobic Denitrification (HN-AD) simultaneously under aerobic conditions. However, the actual product label only claims it eliminates Hydrogen Sulfide (H2S) and mentions nothing about nitrogen. Did I fall into a strain-specific trap, or did I totally misapply this bacteria for an aquarium context?

Would love to hear some thoughts from the microbiology or wastewater crowd here. Where is my logic failing?

Thanks in advance!