By Marco G. Pistrin, Founder and Managing Director, AquaOrganica SRL, Italy
Walk into any aquaculture operation and you’ll find farmers who can quote their dissolved oxygen levels to two decimal places, debate biofilter media surface area calculations with alarming precision and track feed conversion ratios like their mortgage depends on it. Ask them about their alkalinity management protocol and you’ll get a blank stare—or worse, a defensive explanation about how they “check it sometimes” when they “remember to.” Meanwhile, this parameter is being consumed at approximately seven grams per gram of ammonia oxidised, fundamentally altering the chemistry of their system whether they’re paying attention or not.
I’ve walked through too many operations where the biofilter sits there like an underperforming employee – present, technically doing something, but nowhere near its potential. The ammonia levels hover just high enough to matter. The nitrite spikes appear at inconvenient moments. And the farmer, frustrated, starts looking how they should increase the size of the biofilter when the real problem is documented on every water chemistry report they’ve been ignoring: alkalinity bouncing between 80mg/L and 180mg/L (if they are even lucky in some instances!). Apparently, consistency is optional when you’re only trying to run a business.
The nitrifying community in your biofilter isn’t the simple Nitrosomonas-and-Nitrobacter story from the outdated textbooks some of you are still citing. Recent genomic research has revealed that well-functioning freshwater systems are dominated by complete ammonia-oxidising (comammox) Nitrospira species and ammonia-oxidising archaea—organisms adapted to stable, low-ammonia environments. These are specialists that thrive under consistent conditions. When you let your water chemistry parameters swing wildly, you’re actively selecting against the most efficient nitrifiers.
Consider what happens when alkalinity drops below 100mg/L. The pH stability disappears. The buffering capacity that protects your nitrifiers from metabolic acidification vanishes. Multiple studies on recirculating aquaculture system (RAS) operations confirm that maintaining alkalinity at or slightly above 100mg/L (as calcium carbonate) delivers superior ammonia removal rates and stable system pH. Drop down to 10mg/L and steady-state ammonia concentrations climb significantly. The bacteria will adapt to suboptimal conditions because they have no choice, but perhaps we should ask why you’re forcing them to compensate when sodium bicarbonate costs less than your morning coffee.
Temperature management tells a similar story. Nitrifiers perform optimally between 25-30°C, yet systems can routinely operate from as low as five degrees celcius for species like Arctic Charr up to 26°C for yellowtail. It is important to note that bacterial metabolism doesn’t accommodate your production calendar. It slows when temperatures drop. That biofilter handling your ammonia load in cold water underperform compared to even five degrees warmer, at the same stocking density—not because the bacteria died, but because basic biochemistry still applies even when it’s inconvenient.
Then there’s source water. Municipal suppliers aren’t trying to help you farm fish; they’re preventing human disease outbreaks. That means chlorine or chloramine in your makeup water. Chloramine is particularly problematic because it’s designed to persist in distribution systems, and when it degrades, it releases ammonia, the very compound you’re spending thousands of dollars trying to remove. Continuous low-level chloramine exposure stresses nitrifying communities, yet operations routinely add untreated municipal water directly to their systems, then act surprised when biofilters never fully mature or when unexplained nitrite spikes appear after water exchanges. The mystery is truly baffling.
The fixes aren’t complicated: activated carbon filtration, chemical dechlorination or holding makeup water for 24-48 hours. Basic interventions that somehow remain beyond the capacity of operations that can afford sophisticated monitoring equipment but apparently not a holding tank.
Salinity shifts present another overlooked challenge. Freshwater biofilters develop fundamentally different microbial communities than marine systems. Comammox Nitrospira dominating freshwater filters are essentially absent in full seawater, replaced by ammonia-oxidising archaea and bacteria. Gradually increasing salinity for euryhaline species doesn’t just stress your fish—it forces complete microbial community restructuring in your biofilter. But sure to plan ahead for this!
The frustrating reality is that the knowledge exists to optimise these systems. We understand that microbially mature biofilters, where stable populations have established over months or years, dramatically outperform newly cycled systems in both conversion rates and stress resistance. We know that consistent water chemistry allows the most efficient nitrifying species to dominate. We have accessible technology to monitor and control alkalinity, temperature and source water quality. You also have the ability to purchase isolated nitrifying bacteria to seed and to help promote the ‘good bacteria’ in your biofilters! We can work smarter and take advantage of these products that actually exist on the marketplace.
Yet economic performance suffers because biofilters are treated as mysterious black boxes that should ‘just work’ rather than as biological systems requiring proper environmental management. Every day ammonia runs at 0.3mg/L instead of 0.05mg/L costs you in feed conversion, stress-related mortality and lost growth. Every nitrite spike forcing reduced feeding appears directly in harvest projections. These aren’t abstract water quality concerns; they’re line items in your financial statements.
The opportunity here isn’t revolutionary technology. It’s applying existing knowledge consistently. Test alkalinity daily. Maintain it at target levels proactively. Treat source water. Adjust expectations based on actual water temperature and salinity. Provide your microbial community with stable conditions that select for efficient nitrifying consortia.
A well-managed biofilter isn’t just about water quality. It’s about economic performance. Maybe that’s worth prioritising over the next biofilter media debate.
