Pits or lesions on the head

Small pitted craters in the flesh above or behind the eye, often in cichlids and discus — hole-in-the-head, linked to Hexamita and long-term stress. Compare your fish with the reference photo above and cross-check your logged parameters in Aquarium Tracker before medicating.

SymptomPits or lesions on the head

CausesChronically elevated nitrate and dissolved organics / Hexamita, an internal protozoan that proliferates under stress

TreatmentBring nitrate down with larger and more frequent water changes — this alone often halts progression / Improve diet variety and quality, including vitamin-enriched foods

PreventionQuarantine new fish; zero ammonia & nitrite

What causes pits or lesions on the head?

Chronically elevated nitrate and dissolved organics
Hexamita, an internal protozoan that proliferates under stress
Poor diet lacking variety or vitamins
Activated carbon and stray voltage are sometimes implicated, though evidence is debated

What to check before medicating

What to measure	Typical target	What an off reading points to
Nitrate (NO₃⁻)	5–20 ppm planted · under 10 ppm reef	Climbing nitrate signals more waste going in than water changes and plants export. Near zero in a planted tank starves plants and favours algae.
Ammonia (NH₃/NH₄⁺)	0 ppm	Anything above zero means the biological filter cannot keep up. Toxic to fish long before it is high enough to feed algae.
Nitrite (NO₂⁻)	0 ppm	A reading above zero points to an immature or disrupted filter — common after a media change, medication, or a large clean.
Feeding amount and frequency	eaten within 2–3 minutes, no residue	Uneaten food is the most common hidden nutrient source. It breaks down out of sight in substrate and filter media.
Filtration and flow	4× tank volume per hour freshwater · 6×+ reef	Low turnover leaves dead spots where detritus settles. Check working flow rather than the box rating, which assumes clean media and no head height.
Stocking level and mix	suits volume, footprint and temperament	Crowding raises waste and stress together, which is why disease often follows a new addition rather than a parameter change.

Take these readings first. A large share of what looks like disease is a water quality problem, and medicating a tank whose ammonia is climbing treats the symptom while the cause keeps working.

Treatment steps

Bring nitrate down with larger and more frequent water changes — this alone often halts progression
Improve diet variety and quality, including vitamin-enriched foods
Reduce crowding and aggression, which sustain the underlying stress
Existing pits heal slowly and may scar even once the cause is corrected
Advanced cases typically need targeted anti-protozoal treatment under specialist guidance

Prevention

Feed a varied, vitamin-rich diet — long-term nutrition matters more here than any treatment
Reduce chronic stress: stable parameters, adequate cover, and stocking suited to the species
Avoid overstocking; crowding raises waste and stress at the same time
Feed only what is eaten in a few minutes, and remove the rest

Frequently asked questions

Is pits or lesions on the head contagious to my other fish?

Not strongly. It is generally linked to diet, water quality and long-term stress rather than transmission.

How quickly do I need to act?

Not urgent, but do not ignore it. Progression is slow and reversal depends on sustained diet and water quality changes.

Should I treat in the display tank or a hospital tank?

A separate hospital tank is preferable where the fish is well enough to move: doses are easier to control, and many medications harm invertebrates, plants or the biological filter. Treat in the display only when the whole tank is affected or moving the fish would add more stress than the treatment removes.