Why Aquarium Water Smells Bad: Rotten-Egg, Musty and Fishy Odours

A rotten-egg smell signals hydrogen sulfide from oxygen-free pockets and is an emergency; musty odours come from microbes; a strong fishy or foul smell usually means decay.

The type of smell points to the cause. A rotten-egg smell means hydrogen sulfide (H2S) produced in oxygen-free pockets of substrate or sediment, and it should be treated as an emergency. A mild earthy or musty smell comes from microbial compounds such as geosmin and is usually harmless, while a strong fishy or foul smell almost always means something is decaying: a dead fish, rotting plants, excess food or a clogged filter.

Rotten-egg smell: hydrogen sulfide

Hydrogen sulfide has a characteristic rotten-egg odour that humans detect at very low concentrations; Wikipedia gives an odour threshold of 0.00047 ppm in air. It is produced by sulfate-reducing bacteria that use sulfate instead of oxygen to break down organic matter where oxygen is absent (Wikipedia; C. E. Boyd, Global Aquaculture Advocate). The MSD Veterinary Manual places it in poorly maintained tanks and ponds whose sediments are not cleaned regularly, creating anoxic areas, and names well water as another common source. The guide Redox Chemistry in Aquariums: Electron Acceptors, Substrate Zones and Sulfide explains why deep, undisturbed layers turn sulfidic.

Why H2S is dangerous

It blocks cellular respiration by binding to cytochrome enzymes in the mitochondria (Wikipedia; Boyd).
The MSD Veterinary Manual reports acute mortality at 0.5 mg/L and states that any detectable hydrogen sulfide should be considered a major problem. Boyd cites 96-hour LC50 values of 20–50 µg/L for freshwater fish and 50–500 µg/L for marine species, with long-term exposure ideally kept below 2 µg/L and 5 µg/L respectively.
Acute exposure causes sudden death; chronic exposure causes lethargy and poor appetite and growth (MSD Veterinary Manual).
Lower pH makes it worse. H2S is a weak acid with a pKa of about 7.0 (Wikipedia), and only the un-ionised H2S form is toxic (Boyd). In Boyd's table for freshwater at 26 °C, about 50 % of total sulfide is H2S at pH 7.0 but about 9 % at pH 8.0.

Removing the source of H2S

Increase aeration and surface agitation. Oxygen depletion is what allows sulfide to form, and Boyd lists aeration as a core mitigation.
Feed conservatively, so uneaten food does not accumulate as fuel for sulfate reduction (Boyd).
Remove accumulated organic sediment. Boyd lists sediment removal; the MSD Veterinary Manual links H2S to sediments that are not cleaned regularly. Siphon detritus regularly so that it cannot build up again.
Test well water before use if it is the water source, because it can carry H2S (MSD Veterinary Manual).
Keep pH from falling, since acidic water raises the toxic H2S fraction (Boyd; see pH Keeps Dropping: Causes of a pH Crash and How to Stabilise It).

Large recirculating and saltwater systems face the same chemistry at larger scale; the guide Hydrogen Sulfide Risk in RAS and Saltwater Systems covers it. A veterinary-reviewed guide also notes that some water treatments and medications can themselves smell of sulfur after dosing, which is different from a smell rising from the substrate (The Vet Desk).

Musty or earthy smell

Geosmin gives a distinct earthy or musty odour and is detectable by people at 0.006–0.01 µg/L in water; it is made by cyanobacteria and by actinomycetes, particularly Streptomyces, and often occurs together with 2-methylisoborneol (Wikipedia). In recirculating aquaculture, myxobacteria are among the most abundant geosmin-producing groups and have been isolated from these systems (Europe PMC, 2025 study of RAS myxobacteria). A faint earthy smell in an established tank is commonly the normal smell of its bacterial community (The Vet Desk). A stronger, persistent musty smell suggests a growing population of geosmin producers, such as cyanobacteria (Wikipedia), and a reason to look for and remove their growth. Activated carbon can reduce geosmin somewhat (Wikipedia); the guide Activated Carbon in Aquariums describes how carbon works and when it is exhausted.

Fishy or foul smell

A dead fish. A potent fishy odour is a common sign of a decomposing fish hidden behind decor or in a filter; remove it at once (The Vet Desk), then test ammonia, because bacterial decomposition of organic waste produces it (SRAC 451).
Rotting plants or algae. Remove decaying leaves and stems (The Vet Desk).
Waste trapped in the substrate and overfeeding. Siphon the substrate during water changes and feed less (The Vet Desk).
A clogged or failed filter. Clean the mechanical media in tank water so that the nitrifying bacteria are not killed by chlorinated tap water (SRAC 4502 notes that chlorine kills them).

When it is disease

Odour itself is not a disease, but its causes harm fish. Sudden deaths after a rotten-egg smell or after disturbing the substrate point to hydrogen sulfide poisoning. Lethargy, gasping and poor appetite in a smelly tank may reflect ammonia, nitrite or low oxygen; see Ammonia vs Ammonium: How pH and Temperature Set the Toxic Fraction and Nitrite Toxicity and Chloride Protection: Brown Blood Disease Explained. If fish show ulcers, frayed fins or white spots, use the disease article that matches the signs.