Most fish “fungus” problems show up at the exact moment you don’t want surprises: a new fish has just come home, a favourite has a cottony patch on its fin, or a tank that looked stable yesterday suddenly has clamped fins and sore-looking skin.
These infections are often secondary—an opportunistic bloom on damaged skin or stressed fish—so the real risk isn’t just the fuzzy patch itself, but what it signals about water quality, handling, crowding, or an underlying disease. The safest approach is to slow down, confirm what you’re seeing, and fix the conditions that let it take hold before you reach for a treatment.2, 3
What people mean by “fungus” in aquarium fish
In home aquariums, “fungus” usually describes a white-to-grey, cotton-wool growth on skin, fins, or eggs. Often it’s caused by water moulds (oomycetes) such as Saprolegnia, which behave like fungi in aquariums and tend to colonise damaged tissue or dead eggs.4
True fungal infections do occur, but they’re less commonly the primary problem in otherwise healthy, well-kept ornamental fish. The practical takeaway is the same: treat the fish and correct the husbandry issue that made the outbreak possible.2, 4
Common “fungal” conditions (and a key correction)
The names used in shops and forums can be misleading. Some conditions often bundled under “fungus” are not fungal at all, and some need veterinary diagnosis to separate them from lookalikes.2
Saprolegniasis (water mould; “cotton wool disease”)
Typical signs include pale, cottony tufts on fins, skin, or around an injury. It commonly follows net damage, fighting, transport stress, or chronically poor water quality.4
Branchiomycosis (gill rot)
This is a serious gill disease seen more often in aquaculture than in home tanks. It can cause respiratory distress and sudden losses, and it’s not something to guess at from appearance alone.5
Ichthyophonus (not a “fungus on the skin”)
Ichthyophonus causes a systemic infection—often with chronic wasting and internal lesions—and is not the same thing as a surface cottony growth. If a fish has persistent illness with unclear cause, a laboratory diagnosis is the only reliable way to sort fungal-like organisms from other serious diseases.6
Signs that fit a fungal/water-mould problem
Watch for:
- white, grey, or off-white “cotton” patches on fins or body
- skin that looks roughened, thickened, or ulcerated (often with a fuzzy edge)
- frayed fins that don’t improve once water quality is corrected
- fish spending more time resting, hiding, or being pushed around by tankmates
These signs overlap with bacterial disease, parasites, and simple injury. Visual appearance alone can be a trap.2
Diagnosis: when to treat at home, and when to get help
If there’s a small patch on an otherwise active fish and you can clearly link it to recent injury or transport, you can often respond with improved water quality, reduced stress, and careful supportive care while you observe closely.
If there are multiple fish affected, rapid spread, unexplained deaths, or gill/breathing signs, treat it as potentially serious. NSW DPI advises that unusual signs or unexplained deaths (particularly in cultured or wild fish) should be reported promptly, and Australia’s federal guidance also emphasises reporting unusual aquatic animal disease events (including via the Emergency Animal Disease Hotline).1, 7
Causes and risk factors (what lets it take hold)
These organisms are often present in aquatic environments. Outbreaks are more likely when fish are stressed or the tank is working against them:
- poor water quality (ammonia/nitrite spikes, high organic waste load)
- injury (net damage, nipping, abrasion on décor)
- overcrowding and chronic low-level stress
- temperature swings and unstable conditions
- new arrivals without quarantine introducing pathogens (or simply arriving stressed and vulnerable)
NSW DPI notes that many “named” aquarium illnesses are symptom labels rather than a confirmed single cause, and that proper diagnosis may require microscopy or specialist tests.2
First response: what to do when you spot “fungus”
- Stop and observe for 5 minutes. Note breathing rate, balance, appetite, and whether tankmates are nipping.
- Test the water now (at minimum: ammonia, nitrite, nitrate, temperature). Poor water is a common driver of recurring “fungus-like” outbreaks.
- Do a partial water change if parameters are off, and clean obvious waste without stripping the filter of beneficial bacteria.
- Isolate if practical (a simple hospital tank reduces spread and lets you treat without stressing the whole system).
- Take clear photos each day. Progression (or lack of it) is diagnostic information.
Treatment options (use the right tool, not a random one)
Medication choice depends on the organism and the fish species, and some products used in aquaculture are not suitable for casual use in home tanks. Avoid the common mistake in older advice: antibiotics do not treat fungal/water-mould infections. They are for bacterial disease and should be used under veterinary direction when possible.2
Antifungal/anti–water mould approaches used in managed settings
In aquaculture contexts, hydrogen peroxide is used as an immersion treatment for certain external infections, including saprolegniasis of freshwater-reared finfish eggs, with species sensitivity and dosing considerations.4
For imported ornamental fish during Australian post-arrival quarantine, the Department of Agriculture, Fisheries and Forestry (DAFF) maintains a list of chemicals that are approved for use in quarantine settings under specific conditions and directions.8
What to do in a home aquarium
For home aquariums, the safest baseline is:
- prioritise water quality and stress reduction first
- treat in a hospital tank where possible
- follow product directions exactly and avoid stacking multiple medications “just in case”
- consult an aquatic-experienced veterinarian for persistent or spreading cases
NSW DPI specifically cautions that gross signs alone should not be used to diagnose and treat suspected fish disease without appropriate training and diagnostics.2
Prevention that actually holds up
Quarantine new fish
Quarantine isn’t about perfection; it’s about time. A short isolation period lets transport stress settle and gives you a window to notice disease before it reaches the display tank. It also lets you treat one fish without dosing an entire community tank.
Keep a stable, clean system
NSW DPI’s hobbyist guidance emphasises practical routines that reduce stress and disease pressure—regular partial water changes, not overfeeding, and avoiding overcrowding.2
Dispose of fish and water responsibly
Aquarium fish and their water can carry diseases that threaten waterways and aquaculture if released. DAFF advises never releasing aquarium fish into waterways and disposing of aquarium water appropriately (not into stormwater drains or local waterways).7
Buying fish online: the real risks (and how to reduce them)
Online buying isn’t automatically unsafe, but the risk profile is different: longer transport times, temperature swings, and delayed recognition of illness. Those pressures can tip a fish into opportunistic “fungus-like” outbreaks even when the original stock was reasonable.
Simple safeguards:
- choose sellers who ship with temperature control appropriate to the season and your location
- inspect the fish immediately on arrival (photos help if you need to raise an issue)
- quarantine by default, even if the fish “looks fine”
- avoid adding multiple new fish from different sources to the same tank on the same day
When to escalate quickly
- multiple fish affected within 24–48 hours
- breathing distress, gasping, or gill damage
- rapid tissue breakdown, deep ulcers, or sudden deaths
- you keep outdoor ponds that could overflow to stormwater or waterways
If you suspect a serious disease event, follow official reporting advice. DAFF lists the Emergency Animal Disease Hotline (1800 675 888) for unusual symptoms in aquatic animals, and NSW DPI provides guidance for reporting aquatic diseases and unusual deaths.1, 7
Final thoughts
Most aquarium “fungus” is a signal flare: a fish has been stressed, injured, or kept in water that isn’t quite right. When you correct the underlying conditions—clean water, steady temperature, sensible stocking, gentle handling—true fungal/water-mould problems become less common and easier to contain. When signs are widespread or severe, resist guesswork and treat it as a diagnostic problem first, not just a medication problem.2
References
- NSW Department of Primary Industries: Report an aquatic pest or disease
- NSW Department of Primary Industries: Caring for your pet fish
- Australian Government DAFF: Approved chemicals for ornamental fish (post-arrival quarantine)
- Merck Veterinary Manual: Therapeutic considerations in aquaculture (includes hydrogen peroxide use for fungal infection/saprolegniasis of eggs)
- FAO: Health management and biosecurity maintenance in fish farming (includes discussion of gill diseases such as branchiomycosis)
- Iowa State University, Center for Food Security and Public Health: Ichthyophonus hoferi factsheet
- Australian Government DAFF: How you can protect Australia’s aquatic animal health
- Australian Government DAFF: Industry Advice Notice 41-2025 (live marine ornamental fish quarantine release conditions)
- Australian Government DAFF: Australia’s National List of Reportable Diseases of Aquatic Animals (June 2025)
Veterinary Advisor, Veterinarian London Area, United Kingdom