How to Set Up a Quarantine Tank: Protecting Your Aquarium Investment

A quarantine tank (QT) is the single most important tool for maintaining a healthy aquarium. This separate, simple tank isolates new fish, sick fish, or injured fish—preventing disasters in your main display tank.

Despite its importance, many hobbyists skip quarantine, only to regret it when disease wipes out their entire tank. This guide shows you how to set up an effective quarantine system that saves fish, money, and heartache.

Why You Need a Quarantine Tank

Disease Prevention:

New fish often carry hidden diseases or parasites
Quarantine reveals problems before they spread
Treatment in QT is easier than in a planted, decorated main tank
Prevents losing entire established communities

Observation Period:

2-4 weeks allows diseases to manifest
Many pathogens have incubation periods
Fish under stress from transport are most vulnerable
Early detection means easier treatment

Acclimation Support:

New fish often won’t eat initially
QT allows monitoring of feeding behavior
Ensures fish are healthy before adding to community
Reduces aggression during introduction

Treatment Capability:

Bare tank makes dosing medication simple
No carbon to remove treatments
Easy water changes during treatment
Plants and decorations don’t absorb medications

Stress Reduction:

Injured or bullied fish recover in peace
Pregnant fish can give birth safely
Sick fish receive focused care
Main tank remains stable and peaceful

The Simple Quarantine Tank Setup

Minimum Requirements

Tank Size:

10-20 gallons for most community fish
29-40 gallons for larger cichlids, goldfish
5 gallons minimum for bettas or single small fish
When in doubt, bigger is better

Essential Equipment:

Sponge filter (air-driven, gentle, safe for medicating)
Heater (adjustable, reliable)
Hiding places (PVC pipes, terracotta pots—easy to sterilize)
Thermometer
Test kit (liquid tests for ammonia, nitrite, nitrate)
Air pump (for sponge filter)

Optional but Helpful:

Bare-bottom or minimal substrate (easier cleaning)
Simple LED light
Net dedicated to QT only
Separate siphon/vacuum

Why Sponge Filters Are Best for QT

Advantages:

Gentle flow won’t stress sick fish
No chemical filtration removes medications
Biological filtration establishes quickly
Safe for fry and weak fish (no intake suction)
Inexpensive ($10-20)
Dual-purpose: Mechanical + biological in one

Setting Up Sponge Filter:

Install in QT tank
Run with air pump
Keep running 24/7 even when empty
Beneficial bacteria stay alive for weeks

Running a “Permanent” Quarantine Tank

The best QT is always ready to go. Here’s how to maintain one continuously:

Continuous Operation:

Keep sponge filter running 24/7
Maintain temperature (72-78°F default)
Test water weekly
Perform water changes every 1-2 weeks

Seeding the Filter:

Run sponge in established tank for 2-4 weeks
Instantly cycles the QT when moved
Can keep spare sponge in main filter always
Swap to QT when needed

Bare-Bottom Benefits:

Easy to see fish waste and uneaten food
Simple to clean with siphon
No gravel to harbor parasites
Easy to catch fish when needed

The Quarantine Protocol

When to Quarantine

Always Quarantine:

All new fish purchases
Fish returning from breeding loans
Fish from unknown/untrusted sources
Wild-caught fish

Consider Quarantine:

Plants (can carry snails, parasites, algae)
Decorations from other tanks
Fish showing any signs of illness

QT Duration:

Minimum: 2 weeks (14 days)
Recommended: 3-4 weeks
High-risk situations: 4-6 weeks
Never less than 2 weeks—many diseases take time to show

Step-by-Step Quarantine Process

Day 1: Arrival

Float bag in QT for 15-20 minutes (temperature acclimation)
Add small amounts of QT water to bag every 5 minutes for 30-45 minutes
Net fish from bag (never pour bag water into QT)
Release fish into QT
Dim lights and leave undisturbed for several hours
Do not feed first day

Days 2-7: Observation

Offer small amounts of food once daily
Observe for: eating, activity level, breathing rate, signs of disease
Test water daily (ammonia can spike quickly)
Perform water changes if ammonia >0.25 ppm
Note any abnormal behavior

Days 8-14: Continued Monitoring

Test water every 2-3 days
Continue observation for disease signs
Increase feeding gradually
Watch for: Ich (white spots), fin rot, fuzzy growths, parasites
Look for flashing (rubbing on objects), clamped fins, lethargy

Days 15-21: Pre-Release Assessment

Fish should be eating well
No signs of disease
Active and behaving normally
Water parameters stable
Ready for main tank if all criteria met

Day 21+: Treatment If Needed

If disease appears, begin appropriate treatment
Extend quarantine duration
Complete full treatment course
Wait 7 days after treatment ends before moving to main tank

Signs to Watch For During Quarantine

Immediate Red Flags:

Clamped fins (fins held tight to body)
Flashing (rubbing against objects)
Rapid breathing or gasping
Lethargy or hiding constantly
White spots (Ich)
Stringy feces (internal parasites)
Visible wounds or fin damage
Fuzzy growths (fungus/bacteria)

Behavioral Changes:

Not eating after 3 days
Sitting at bottom or top exclusively
Erratic swimming patterns
Aggression (if multiple fish in QT)
Color fading or darkening

Medicating in Quarantine

When to Treat:

Visible signs of disease
Preventive treatment for high-risk fish
Parasites observed
Bacterial infections present

Common QT Treatments:

1. Preventive/General:

Aquarium salt (1 tablespoon per 5 gallons)
Reduces stress, helps with osmoregulation
Good for most freshwater fish

2. External Parasites (Ich, Velvet):

Ich-X or similar medication
Raise temperature to 82-86°F (if fish tolerate)
Treatment duration: 7-14 days
Continue 3 days after spots disappear

3. Bacterial Infections:

Kanaplex (kana mycin)
Furan-2
Maracyn products
Follow manufacturer dosing exactly

4. Fungal Infections:

API Fungus Cure
Pimafix
Often combined with bacterial treatments

5. Internal Parasites:

PraziPro (Praziquantel)
Levamisole
Garlic-enhanced food

Treatment Tips:

Always remove carbon from filter during medication
Increase aeration (medications reduce oxygen)
Follow dosage exactly—more is not better
Complete full treatment course even if fish looks better
Test water daily during treatment
Do water changes between doses if instructed

Special Quarantine Situations

Hospital Tank vs. Quarantine Tank

Hospital Tank:

For confirmed sick fish from main tank
Usually smaller (5-10 gallons)
Set up only when needed
May need to cycle with seeded media quickly

Quarantine Tank:

For new arrivals
Larger (10-40 gallons)
Permanent or semi-permanent setup
Always cycled and ready

Breeding/Fry Quarantine

Setup Modifications:

Use sponge filter with fine sponge (protects fry)
Add lots of hiding places
Keep water pristine (daily small water changes)
Feed 3-4 times daily with appropriate fry food
Temperature appropriate for species (often slightly warmer)

Plant Quarantine

Why QT Plants:

Snail eggs hitchhike on plants
Parasites like Ich can transfer on plants
Algae spores present
Some plants carry harmful chemicals

Plant QT Methods:

Method 1: Observation (2 weeks)

Place in separate container
Watch for snails, algae
Rinse thoroughly before adding to main tank

Method 2: Chemical Dip

Hydrogen peroxide dip: 2-3 ml per gallon for 5 minutes
Potassium permanganate dip (follow instructions carefully)
Bleach dip: 19 parts water to 1 part bleach for 2-3 minutes
Rinse thoroughly with dechlorinated water

Method 3: Alum Soak

Alum (pickling spice) 1 tablespoon per gallon
Soak plants for 3 days
Kills snail eggs effectively
Rinse well before adding to tank

Common Quarantine Mistakes

1. QT Tank Too Small

Stresses fish, causes water quality issues
Solution: Minimum 10 gallons for most fish

2. Not Cycled QT Tank

Ammonia spikes harm already-stressed fish
Solution: Keep sponge running or use seeded media

3. Moving Fish Too Soon

Diseases often take 2+ weeks to show
Solution: Minimum 2-week quarantine, preferably 3-4

4. Using Same Equipment

Cross-contaminates between QT and main tank
Solution: Separate nets, siphons, towels

5. Overfeeding in QT

Uneaten food pollutes small tank quickly
Solution: Feed sparingly, remove uneaten food

6. Not Treating the Full Duration

Stopping treatment early allows disease to return
Solution: Always complete full course, plus 3 days

7. Adding to Main Tank When Fish “Looks Better”

Symptoms may be suppressed, disease still present
Solution: Wait full quarantine period, verify health

Water Quality in Quarantine

Testing Schedule:

Days 1-7: Daily ammonia and nitrite tests
Days 8-14: Every 2-3 days
During treatment: Daily testing

Water Change Guidelines:

No medication: 25% every 2-3 days, or as needed for ammonia
With medication: Follow medication instructions (often daily 25-50%)
After treatment: 50% change before returning to main tank

Water Parameters:

Match main tank temperature
Match main tank pH closely
Use same water source as main tank
Ensure no chlorine/chloramine

Budget Quarantine Setup

Essential Costs:

10-gallon tank: $15-25
Sponge filter: $10-15
Air pump: $10-20
Heater: $15-25
PVC pipe hides: $5
Total: $55-90

Money-Saving Tips:

Use storage tote instead of glass tank ($10-15)
Skip substrate entirely
Use items from dollar store for hides
No fancy light needed—simple clip-on LED
Test kit can be shared with main tank

The Cost of NOT Quarantining:

Medication for entire tank: $20-50
Replacing dead fish: $50-200+
Replacing entire colony if wiped out: $100-500+
Emotional cost: Immeasurable

Quarantine pays for itself with the first prevented disaster.

Advanced Quarantine Strategies

Two-Tank System:

QT 1: New arrivals (4 weeks)
QT 2: Treatment tank for sick fish
Prevents medicating healthy new arrivals unnecessarily

Observation Tank:

Small tank for visual inspection
Fish in for 24-48 hours
Then move to main QT or main tank
Quick check for obvious issues

Species-Specific QT:

Saltwater QT (marine fish need separate everything)
Cichlid QT (often larger, more aggressive)
Shrimp QT (very sensitive to medications)

When to Break Quarantine Rules

Never Skip Quarantine:

Fish from pet stores (even “healthy-looking”)
Fish from unknown sources
Wild-caught specimens
Auction or swap meet fish

May Consider Shortening:

Fish from trusted breeder you know
Fish from your own established tanks
Emergency situations (tank crash, etc.)
Even then, minimum 1 week observation

Conclusion

A quarantine tank isn’t optional equipment—it’s essential insurance for your aquarium. The small investment in a simple 10-gallon setup protects hundreds or thousands of dollars in fish, plants, and equipment.

The 2-4 week wait may feel long, but watching disease wipe out a beloved community tank feels infinitely worse. Set up your QT before you need it, keep it running, and use it religiously for every new addition.

Your future self—and your fish—will thank you.

Concerned about fish diseases? Read our aquarium disease identification guide to recognize and treat common ailments.