Freshwater and Saltwater Fish Disease Guide: Identify, Understand and Treat

Fish rarely get sick without warning. Long before a visible spot, ulcer or swelling appears, something in the system has usually shifted — a spike in ammonia, a temperature swing, a new arrival added without quarantine, or a slow decline in water quality that stressed the immune system. By the time symptoms show, you are treating the result of a problem, not the problem itself.

This guide is built to do two things: help you identify what you are actually looking at, and match it to the correct Seachem treatment. It covers nine of the most common freshwater and saltwater conditions, what causes them, what they look like, and how to treat them properly.

A note before you dose anything: correct identification matters more than fast action. Treating fungus with an antibiotic, or bacterial septicaemia with a parasite treatment, wastes time the fish does not have and adds unnecessary chemistry to the tank. Read the symptoms carefully first.

Table of Contents

• Before you treat: five things to check first
• Dropsy
• Popeye (Exophthalmia)
• Gill Flukes
• Hole in the Head
• Bacterial Lesions
• Mouth Rot
• Fungus
• Fin and Tail Rot
• Ich and Velvet
• Quick reference: symptom to treatment
• How to medicate food with Focus
• Setting up a quarantine tank
• Common treatment mistakes
• Frequently asked questions
• Key takeaway

Before you treat: five things to check first

Medication is the last step, not the first. Run through this list before you open a single bottle — in a meaningful number of cases, correcting the underlying condition resolves the problem on its own.

• Test the water. Ammonia and nitrite should read zero. Anything above that is actively damaging gill tissue and suppressing the immune system.
• Check the temperature. Sudden swings are a leading trigger for ich and secondary bacterial infections.
• Look at stocking and aggression. Torn fins, missing scales and localised ulcers are frequently the result of physical damage, not disease.
• Increase aeration. Most medications reduce dissolved oxygen. Add an airstone before you dose, not after the fish start gasping.
• Remove chemical filtration. Activated carbon and resins will strip the medication straight out of the water. Take them out for the duration of treatment.

If ammonia or nitrite are present, dose Seachem Prime to detoxify them immediately, and address the cause. Seachem StressGuard helps reduce stress and supports the protective slime coat while the fish recovers.

Dropsy

Dropsy is not a disease in itself. It is a visible symptom of internal fluid accumulation, usually caused by organ failure — most often the kidneys — following a systemic bacterial infection. It is the most serious condition on this list and the hardest to reverse.

What to look for

• Swollen or bloated abdomen.
• Pineconing scales: scales stand out from the body, giving a pinecone-like appearance when viewed from above.
• Bulging eyes (exophthalmia) caused by internal pressure.
• Lethargy, loss of appetite, and sitting on the substrate.

Why it happens

Chronic poor water quality, prolonged stress, internal bacterial infection or an underlying organ problem. Dropsy is very often the endpoint of weeks of unnoticed decline rather than a sudden event.

Treatment

KanaPlex is the treatment of choice because kanamycin is absorbed effectively and reaches internal tissue. Delivered in food using Focus as a binder, it targets the infection internally rather than relying on absorption from the water column — which is what a systemic infection requires.

Move the affected fish to a quarantine tank if possible. Be realistic: dropsy caught at the pineconing stage has a poor prognosis. Caught early, when there is mild bloating but no scale protrusion, outcomes are considerably better.

Popeye (Exophthalmia)

Popeye describes fluid building up behind or within the eye, pushing it outward. It appears in two distinct forms, and telling them apart tells you what caused it.

What to look for

• Bulging or protruding eye — one or both.
• Cloudy or hazy appearance across the eye surface.
• Swelling around the eye socket, sometimes with redness.
• A white ring or fluid-filled area around the eye.

Reading the pattern

One eye affected usually points to physical injury — a collision with hardscape, netting damage, or aggression from a tankmate — followed by localised infection. Both eyes affected more often indicates a systemic problem: water quality, internal bacterial infection, or in severe cases the early stage of dropsy.

Treatment

KanaPlex is effective against the bacterial component, and combining it with Focus in food helps where the infection is internal. NeoPlex is a strong alternative, particularly for external and gram-negative infections.

Where the cause is injury rather than infection, clean water and reduced stress do most of the work. Check the aquascape for sharp edges and reassess tankmate aggression.

Gill Flukes

Gill flukes are microscopic parasitic flatworms (Dactylogyrus and related genera) that attach to gill tissue. Because they are invisible to the naked eye, they are frequently misdiagnosed as a water quality problem — the fish shows every sign of suffocating, yet the parameters test clean.

What to look for

• Fish appear sluggish, gasp at the surface, or hang near the outflow where oxygen is highest.
• Flashing — rubbing and scraping against rocks, substrate and décor.
• Irritated or reddened gills, with excessive mucus production.
• Rapid or laboured gill movement, twitching, and clamped fins.
• Translucent spots visible in advanced infections.

Why it happens

Flukes almost always arrive on new fish. They multiply rapidly in warm water and in tanks under stress, which is why an outbreak often follows shortly after an unquarantined addition.

Treatment

ParaGuard is the appropriate treatment. It works against external parasites including flukes, and is suitable for both freshwater and marine systems. Increase aeration throughout treatment — the gills are already compromised and dissolved oxygen matters more than usual here.

Repeat dosing is essential. A single treatment kills the attached adults but not necessarily the eggs, so follow the full course to break the life cycle.

Hole in the Head

Also known as Head and Lateral Line Erosion (HLLE), this condition is most commonly seen in cichlids, oscars, discus and marine tangs. It is strongly associated with the protozoan Hexamita, though nutrition and water quality play a significant role in how it develops.

What to look for

• Small pits or holes near the eyes and across the head region.
• Lesions appearing as eroded tissue or shallow craters.
• As the condition worsens, holes deepen and spread along the lateral line.
• Loss of appetite and white, stringy faeces in Hexamita-driven cases.

Why it happens

Contributing factors include poor diet lacking in vitamins and minerals, chronic nitrate accumulation, activated carbon in some marine cases, and prolonged stress. The parasite is often present in low numbers in healthy fish and only becomes a problem when the immune system is compromised.

Treatment

MetroPlex is the standard treatment. Metronidazole is most effective when delivered in food using Focus, since the target organism is internal.

Treatment alone will not fix the underlying cause. Improve the diet with quality frozen and vitamin-enriched foods, increase water change frequency to bring nitrates down, and keep them there.

Bacterial Lesions

Open sores, ulcers and reddened, inflamed patches on the body — often described as ulcer disease or bacterial septicaemia. These are typically caused by Aeromonas, Pseudomonas or Vibrio species that opportunistically colonise damaged tissue.

What to look for

• Open sores or ulcers on the body.
• Reddened patches or inflamed areas, sometimes with visible blood streaking.
• Loss of scales or skin erosion around the lesion.
• White or grey patches with ragged edges.
• Necrotic (dead) tissue around the wound.

Why it happens

Almost always secondary. A wound from aggression, netting, transport, a parasite bite or rough décor breaks the protective slime coat and skin, and bacteria already present in the water colonise the opening. Poor water quality accelerates the process dramatically.

Treatment

NeoPlex is well suited here — neomycin targets the gram-negative bacteria responsible for most ulcer-type lesions. For deep or advanced ulcers, combining it with Focus in medicated food improves the outcome by treating the infection systemically.

StressGuard is useful alongside treatment — it helps seal the wound and supports slime coat regeneration.

Mouth Rot

Mouth rot — often called mouth fungus or cotton wool disease — usually is not a fungus at all. It is most commonly caused by Flavobacterium columnare, a bacterium that produces cotton-like growths easily mistaken for a fungal infection. This distinction matters: treating it as a fungus will not work.

What to look for

• White or greyish film around the mouth.
• Cotton-like growths that resemble fungus.
• Swollen lips or mouth area.
• Erosion or ulceration around the mouth — the lips may appear to rot away.
• Difficulty eating, and refusal of food.

Why it happens

Columnaris thrives in warm water with high organic load and low oxygen. It is highly contagious and can progress very quickly — in severe outbreaks, fish can be lost within 24 to 48 hours. Treat it as urgent.

Treatment

SulfaPlex, PolyGuard and NeoPlex are all effective options. PolyGuard is a broad-spectrum choice when you are not certain whether bacteria, parasites or both are involved.

Lowering the temperature slightly slows columnaris progression in freshwater tanks — but only do this if the species tolerates it. Improve oxygenation and increase water changes at the same time.

Fungus

True fungal infections (Saprolegnia and related genera) appear as distinct cotton-like growths. Genuine fungus is almost always secondary — it colonises tissue that is already damaged or dying.

What to look for

• White, grey or pale cotton-like growths on the skin, fins, mouth or gills.
• Growth may start as fine threads and build into tufts or patches.
• Localised swelling where the fungus is growing.
• Clearly defined, fluffy texture — distinct from the flatter, film-like appearance of columnaris.

Why it happens

Fungal spores are present in every aquarium. They only take hold on injured tissue, dead tissue, or fish with a severely weakened immune system. Unfertilised eggs and untreated wounds are the most common starting points.

Treatment

ParaGuard is a reliable first choice for external fungal infections. PolyGuard, SulfaPlex, NeoPlex and KanaPlex are also effective, particularly where a bacterial component is present alongside the fungus.

Because fungus is secondary, always identify and correct the original injury or stressor. Treating the fungus without addressing the cause invites a repeat.

Fin and Tail Rot

One of the most common conditions in the hobby, and one of the most treatable when caught early. Fin rot is a bacterial infection that progressively erodes fin tissue from the edges inward.

What to look for

• Fraying or ragged edges on fins and tail.
• Discolouration at fin edges — often white, grey or red.
• Fins or tail becoming visibly shorter over time as tissue disintegrates.
• Bloody streaks or inflamed fin bases in advanced cases.

Why it happens

Poor water quality is the leading cause, followed by fin nipping from tankmates, physical damage, and stress from overcrowding or unstable parameters. Long-finned species such as bettas, guppies and fancy goldfish are particularly susceptible.

Treatment

ParaGuard, NeoPlex, SulfaPlex, KanaPlex and PolyGuard are all effective. For mild early cases, improved water quality plus ParaGuard is often sufficient. For advanced rot reaching the fin base, step up to KanaPlex or NeoPlex.

Fins regrow. New growth appears clear or pale before it colours up, so do not mistake healthy regeneration for continued infection.

Ich and Velvet

Two different parasites, grouped together because they are frequently confused. Both are external protozoan parasites with life cycles that only make them vulnerable to treatment during their free-swimming stage — which is why timing and full courses matter so much here.

Ich (White Spot Disease)

• Small white spots on the body, fins and gills, resembling grains of salt or sugar.
• Spots are individually distinct and clearly raised.
• Flashing and rubbing against objects.
• Rapid gill movement and clamped fins.

Velvet

• A fine, dusty coating across the skin and fins.
• Gold, yellowish or rust-coloured — best seen with a torch shone at an angle in a darkened room, where it appears velvety or powdery.
• Far finer than ich; it looks like a dusting rather than distinct spots.
• Rubbing, flashing, and rapid breathing.

Why it happens

Both are introduced by new fish, plants or equipment. Outbreaks are triggered by stress and temperature swings. Velvet is generally more aggressive than ich and can kill faster, particularly in marine systems.

Treatment

Cupramine is the established treatment for both, especially in marine systems. MetroPlex, ParaGuard and PolyGuard are also used depending on the system and severity.

Critical warning: Cupramine is copper-based and is lethal to invertebrates — shrimp, snails, crabs, corals and other inverts. Never dose it in a reef or invertebrate tank. Copper is also adsorbed by rock and substrate, making it very difficult to remove afterwards. Treat in a bare-bottom quarantine tank wherever invertebrates are involved.

Complete the full course even after visible spots disappear. Spots vanishing means the parasites have dropped off the fish to reproduce — stopping at that point guarantees reinfection.

Quick reference: symptom to treatment

Condition	Key identifying sign	Seachem treatment
Dropsy	Pineconing scales, bloated abdomen	KanaPlex, Focus
Popeye	Bulging or cloudy eye(s)	KanaPlex, Focus, NeoPlex
Gill Flukes	Gasping and flashing with clean water parameters	ParaGuard
Hole in the Head	Pits and craters on the head and lateral line	MetroPlex
Bacterial Lesions	Open ulcers and reddened, eroded patches	NeoPlex
Mouth Rot	White film or cotton-like growth around the mouth	SulfaPlex, PolyGuard, NeoPlex
Fungus	Distinct cotton-like tufts on skin or fins	ParaGuard, NeoPlex, SulfaPlex, KanaPlex, PolyGuard
Fin and Tail Rot	Fraying, receding fin edges	ParaGuard, NeoPlex, SulfaPlex, KanaPlex, PolyGuard
Ich / Velvet	Salt-like spots (ich) or fine gold dust (velvet)	Cupramine, MetroPlex, ParaGuard, PolyGuard

How to medicate food with Focus

Focus is one of the most useful and most misunderstood products in the Seachem range. It is not a medication on its own — it is a polymer binder that holds medication to food and helps it survive contact with water long enough to be eaten.

This matters because internal infections — dropsy, hole in the head, systemic bacterial infections — respond far better to medication delivered through food than to medication dosed into the water column, where absorption is limited and much of it is wasted.

The method:

• Mix Focus with your chosen medication (KanaPlex or MetroPlex are the usual pairings) at roughly five parts Focus to one part medication.
• Add approximately one measure of the mixture to one tablespoon of food.
• Add a few drops of water and mix into a paste. Let it sit briefly so the binder sets.
• Feed once or twice daily for the recommended treatment period.

Focus also reduces the impact of medication on the biological filter, which is a meaningful advantage when treating an established display tank.

Setting up a quarantine tank

A quarantine tank is the single most effective disease-prevention measure available, and one of the cheapest. It does not need to be elaborate.

• Size: 40 to 80 litres is sufficient for most community fish.
• Filtration: A sponge filter kept permanently seeded in your main tank's sump or filter, ready to move across.
• Substrate: None. Bare bottom is easier to clean and does not adsorb medication.
• Cover: Somewhere to hide — a length of PVC pipe or a plastic plant reduces stress considerably.
• Heater and airstone: Both essential, particularly during treatment.
• Duration: Four weeks minimum for new arrivals. Most conditions will present within that window.

Quarantining also lets you treat a sick fish without dosing medication into an established display tank, where it can damage the biological filter and harm invertebrates.

Common treatment mistakes

Stopping treatment when symptoms disappear

This is the most common error, and it is particularly damaging with ich. Visible spots vanishing means the parasite has entered a different life stage, not that it has been eliminated. Always finish the full course.

Leaving carbon in the filter

Activated carbon and chemical filtration media remove medication from the water almost as fast as you add it. Remove them before dosing, and put them back afterwards to strip out residual medication.

Combining medications without checking

Some combinations are safe and even recommended. Others compound stress or oxygen depletion. If you are unsure, treat one condition at a time, or ask before mixing.

Dosing copper in a tank with invertebrates

Cupramine will kill shrimp, snails, crabs and corals, and copper binds to rock and substrate where it can leach for a long time afterwards. Use a bare quarantine tank.

Treating without identifying the cause

Fungus, fin rot and bacterial lesions are nearly always secondary to something else — injury, aggression, or water quality. Treating the symptom while leaving the cause in place means the problem returns.

Underdosing to be safe

A partial dose is often worse than no dose. It fails to clear the infection and can encourage resistance. Follow the stated dosage for your actual water volume — accounting for substrate and rock displacement.

Frequently asked questions

Key takeaway

Nearly every condition in this guide traces back to the same root causes: water quality, stress, and fish added without quarantine. Medication treats the symptom; husbandry prevents the problem. Test regularly, quarantine new arrivals for four weeks, keep the tank appropriately stocked, and act at the first sign that something is wrong rather than waiting to see whether it resolves.

When treatment is needed, identify the condition properly, remove chemical filtration, increase aeration, and complete the full course. Early, correct action is what separates a fish that recovers from one that does not.

Browse the full Seachem range and our complete aquarium medications selection at Jungle Aquatics. If you are unsure what you are looking at, send us a clear photo and a description of the symptoms — accurate identification is worth more than a fast guess.