Pests are one of the fastest ways for a new reef tank to go from “looking great” to “what is that thing growing?” The good news: you can prevent pests in a reef aquarium with a simple, repeatable routine—buy carefully, inspect thoroughly, mechanically clean, dip appropriately, and quarantine. It won’t make your tank 100% pest-proof, but it will dramatically reduce risk while keeping corals safer.
Why reef tank pests happen (and why prevention wins)
Prevention is easier than treatment. Most reef aquarium pests arrive as hitchhikers on coral, live rock, macroalgae, frag plugs, or even shared bag water from a store or a friend.
What “pests” really are: hitchhikers vs. true outbreaks
- Hitchhiker: A small organism that enters unnoticed (example: aiptasia polyp on a plug).
- Outbreak: The hitchhiker finds good conditions (nutrients, few predators, time) and multiplies.
Many “pests” are only a problem once they spread. Catching them early is the whole game.
The common beginner mistake: adding livestock straight to display
The #1 beginner slip-up is: acclimate → place in display → hope for the best.
That skips the two steps that prevent most problems:
- Close inspection
- Quarantine (QT) long enough to detect and interrupt pest life cycles (especially eggs)
The most common pests to watch for (quick ID)
Below are common reef aquarium pests (plus a few “usually fine” hitchhikers). If you’re unsure, take a clear photo under white light and ask for help before treating.
Aiptasia and majano anemones
- Aiptasia: Small translucent anemone; fast-spreading; stings nearby corals.
- Majano: Similar “pest anemone,” often greener and bubble-tipped.
Early action matters. A single tiny one can become many.
Flatworms (planaria) and red bugs (Acropora)
- Planaria flatworms: Often reddish-brown on sand/glass/coral; can boom in numbers.
- Red bugs: Tiny yellow-red dots on Acropora; Acropora polyps may stay retracted.
Nudibranchs (zoa-eating, monti-eating)
- Zoa-eating nudibranchs: Camouflaged; often match the zoa color.
- Montipora-eating nudibranchs: White/cream; can cause pale bite patches.
Watch for egg spirals/clusters on the underside and edges.
Vermetid snails, bryopsis/hair algae, bubble algae
- Vermetid snails: Little tube “snails” that cast mucus webs; can irritate coral.
- Bryopsis / hair algae: Often hitchhikes in bases and plugs; can spread if nutrients/light allow.
- Bubble algae (Valonia): Green bubbles; can multiply if popped and spread (not always, but treat carefully).
“Helpful” hitchhikers that are usually fine (copepods, feather dusters)
Not everything is bad:
- Copepods/amphipods: Great clean-up and fish food.
- Feather duster worms: Usually harmless filter feeders.
- Sponges (small): Often beneficial if not smothering anything.
Before you buy: prevention starts at the store
Your best pest-control tool is your wallet. If the system looks risky, don’t bring it home.
What to ask the seller (system history, pest events, dip practices)
Ask simple questions:
- “Do you dip or quarantine corals before sale?”
- “Any recent issues with aiptasia, flatworms, or nudibranchs?”
- “Is this frag from a shared system or an isolated frag tank?”
If they don’t know, assume higher risk and plan a stronger at-home process.
What to look for in the coral tank (aiptasia, algae, dead spots)
Scan the tank itself:
- Look at glass corners and overflow for aiptasia/majano
- Look for bubble algae and thick turf algae
- Watch for dead spots with detritus buildup (often pest-friendly)
If you see pests in the system, you can still buy—but only if you’re prepared to quarantine and treat.
Choosing frags vs. colonies vs. wild/import pieces (risk level)
Here’s a practical risk comparison for beginners:
| Option | Pest Risk | Why | Beginner Tip |
|---|---|---|---|
| Tank-raised frags (from trusted source) | Low–Medium | Smaller surface area; often more observed | Still inspect plug/base closely |
| Larger colonies | Medium–High | More hiding places; harder to dip evenly | Consider trimming and re-mounting |
| Wild/import pieces | High | Less predictable; more hitchhikers | Only if you can quarantine confidently |
At-home inspection: how to check corals and rock safely
Do your inspection before the coral goes into any tank (display or QT). Set up a clean, well-lit workspace.
Tools checklist (white tray, flashlight, magnifier, tweezers)
- White tray or white bowl (makes pests visible)
- Small flashlight (phone light works)
- Magnifying glass or clip-on macro lens
- Tweezers and a soft toothbrush
- Turkey baster (for blowing pests off)
- Gloves and eye protection (especially with zoanthids)
- 2–3 containers of clean saltwater (same salinity/temp as your tank)
Safety note: Zoanthids can contain palytoxin. Don’t scrub or cut them with bare hands. Avoid aerosolizing water (no hot running water, no aggressive brushing outside water). Keep pets/kids away during handling.
Step-by-step visual inspection routine
- Match water first: Use clean saltwater at your tank’s salinity (typically 34–35 ppt) and temperature (commonly 24–26°C / 75–79°F).
- Inspect under white light: Blue lighting hides pests and eggs.
- Examine the base, plug, underside, and crevices:
- Underside edges of encrusting corals
- Frag plug seams and holes
- Any shaded areas
- Look for eggs and damage:
- Egg spirals/clusters (often nudibranch eggs)
- Bite marks, missing tissue, pale patches
- Mucus webs (often vermetids)
- Blast gently with a turkey baster into the tray and watch what falls off.
Mechanical cleaning basics
Mechanical removal is underrated. It’s often the least stressful “treatment” when done gently.
- Remove frag plugs when possible
- Many pests and algae live on/inside plugs.
- If the coral is easily separated, re-mount to a fresh plug or small rock.
- Scrape suspicious spots; rinse in clean saltwater
- Use tweezers or a soft toothbrush (underwater).
- Rinse in a separate container so you don’t reintroduce debris.
- When to trim the base to reduce hitchhikers
- If the base is encrusted onto an old plug with algae or pests, trimming can be safer than trying to “clean it all.”
- If you cut coral, use proper tools and stable conditions (avoid cutting stressed, freshly shipped pieces).
Coral dipping 101 (beginner-friendly, realistic expectations)
Dips are helpful, but they’re not magic. Think of them as a pest reduction step, not a guarantee.
What dips can and can’t do (eggs often survive)
- Can help with: mobile pests (some flatworms, small nudis, some crustaceans)
- Often cannot kill: eggs (nudibranch and some worm eggs commonly survive)
- Cannot fix: pests living deep in rock, heavy algae rooted in pores, or system-level issues
This is why quarantine plus repeat inspections matter.
Common dip types and when to use them
- Commercial coral dips (general-purpose)
- Good beginner default for many frags.
- Follow label directions exactly.
- Iodine-based dips (tissue support, mild pests)
- Often used for coral stress and light pest pressure.
- Not a “kill everything” solution.
- Targeted treatments (only when you know the pest)
- Use when you’ve identified the pest and understand risks.
- Some treatments can be harsh, especially on sensitive corals.
Safety note: Never mix dip chemicals. Don’t improvise concentrations. If a product says “X mL per liter,” measure it.
Safe dip workflow
A simple, repeatable workflow:
- Set up containers
- Container A: dip solution (correct dose)
- Container B: rinse #1 (clean saltwater)
- Container C: rinse #2 (clean saltwater)
- Dip with a timer
- Use the product’s recommended time (do not guess).
- Gentle agitation
- Swish the coral occasionally.
- Use a turkey baster to blow between branches and under edges.
- Rinse thoroughly
- Move coral through rinse #1 and rinse #2.
- Discard dip water—do not pour into any aquarium.
- Then quarantine
- Dipping is not a replacement for QT.
Mistakes to avoid
- Overdosing “just to be safe”
- Dipping too long
- Dipping multiple times back-to-back when the coral is already stressed
- Dipping freshly shipped corals that are clearly struggling (stabilize first in QT with good flow and stable parameters)
Quarantine: the best way to “avoid pests as much as possible”
If you want the biggest improvement in pest prevention, start quarantining corals. It doesn’t need to be fancy.
The simplest coral quarantine setup (low cost)
Beginner-friendly coral QT basics:
- Small tank or food-safe container (10–20 gallons is common)
- Heater + thermometer
- Small powerhead for flow
- Simple light (appropriate for your coral types)
- Frag rack
- Lid (reduces evaporation and prevents contamination)
Keep QT stable:
- Salinity: 34–35 ppt
- Temperature: 24–26°C / 75–79°F
- Alkalinity: commonly 7–9 dKH (match your display as closely as possible)
- Calcium: often 400–450 mg/L
- Magnesium: often 1250–1400 mg/L
You don’t need “perfect numbers,” but you do need stability.
How long to quarantine (and why “multiple weeks” matters)
A practical beginner target: 4–6 weeks.
Why it helps:
- Many pests have egg stages that hatch later.
- A longer QT gives you time to spot patterns: bite marks, new algae growth, nighttime activity.
Observation routine
Keep it simple and consistent:
- Daily quick look under white light (30–60 seconds)
- Night checks 1–2x per week (many pests are nocturnal)
- Re-dip schedule to break egg cycles
- A common approach is an initial dip, then another dip 5–10 days later, plus manual egg removal if you see eggs.
- Always follow product directions and don’t over-stress corals with excessive dipping.
Quarantine for fish vs. coral (different goals)
- Fish QT: often focuses on disease observation and prevention; may include medication (separate topic).
- Coral QT: focuses on pest observation, egg removal, and controlled dipping.
Don’t combine fish and coral QT in one system if you plan to medicate fish.
Managing risk with live rock, sand, and macroalgae
Corals aren’t the only source of hitchhikers on live rock. Macroalgae can also import pests.
“Wet” vs. “dry” rock: trade-offs
- Wet/live rock
- Pros: faster biodiversity, often faster “mature” feel
- Cons: higher hitchhiker risk (aiptasia, algae, crabs, worms)
- Dry rock
- Pros: fewer pest imports
- Cons: slower biodiversity; can take longer to stabilize
For beginners who want fewer surprises, dry rock is often easier—just expect a slower “living” ecosystem at first.
Adding macroalgae safely (especially from refugiums)
Macroalgae (like Chaetomorpha) can carry:
- Aiptasia
- Bubble algae
- Bristle worms
- Flatworms
Safer approach:
- Rinse and inspect in a white container.
- Consider a short observation period in a separate container before adding to your refugium.
Avoiding cross-contamination (shared tools, water transfer)
This is an easy win:
- Don’t share frag racks, tweezers, or brushes between tanks without rinsing and drying.
- Avoid transferring store bag water into your system.
- Label QT tools separately.
If a pest slips through: early response plan
Even with good habits, pests can appear. Early control is much easier than “full outbreak” control.
Contain first: stop trading frags, isolate, reduce spread
- Stop moving frags between tanks.
- If possible, move the affected coral to QT.
- Increase inspection frequency under white light.
Quick actions by pest
Aiptasia: targeted treatment options and prevention of spread
- Treat early when it’s one or two.
- Use a targeted method (commonly gels/pastes designed for aiptasia).
- Don’t scrape in-tank (fragments can spread).
- Recheck the area over the next 1–2 weeks.
Flatworms: siphoning + carbon + careful treatment
- Siphon visible flatworms.
- Run activated carbon (especially if treating—some flatworms can release toxins when dying).
- Follow treatment directions carefully and prepare for water changes.
Nudibranchs: manual removal + repeat dips + quarantine
- Manually remove adults.
- Remove eggs (scrape gently off the underside).
- Repeat dips on a schedule to catch hatchlings.
- Keep the coral in QT until you’ve had multiple “clean” inspections.
When to ask for help (photos, microscope shots, timeline)
Ask for help when:
- You can’t identify the pest
- The coral is rapidly losing tissue
- Treatments aren’t working
Provide:
- Clear photo under white light
- Close-up of underside/base
- Timeline (when added, when symptoms started)
- Current parameters (dKH, ppt, NO3 mg/L, PO4 mg/L)
Reef Buddy tracking tips (so you spot problems sooner)
Prevention gets easier when you track what you added and when.
Log new additions and “inspection/dip/quarantine” steps
In Reef Buddy, create a consistent entry each time you add anything:
- Source (store, trade, online)
- Date added
- “Inspected / mechanically cleaned / dipped / quarantined” (yes/no)
- Notes on what you saw (eggs, algae, bite marks)
Add photo notes for before/after comparisons
Take quick photos:
- Day 0 (arrival)
- After dip
- Weekly in QT
Photos help you notice subtle changes like new bite marks or new algae sprouting from a plug.
Set reminders for re-dips and quarantine milestones
Use reminders for:
- Re-dip day (example: day 7–10)
- Weekly night inspection
- QT graduation day (4–6 weeks)
Shrimpy’s tip: reminders reduce “I’ll do it later,” which is when pests usually win.
Beginner checklist (printable-style wrap-up)
Use this as your “pest prevention flow” for every coral, rock, or macro purchase.
Buying checklist
- Ask about pests and dip/QT practices
- Inspect the store system for aiptasia and algae
- Prefer tank-raised frags when possible
- Avoid buying from systems with obvious pest outbreaks (unless you can QT confidently)
Inspection + cleaning checklist
- Inspect under white light (base, plug, underside)
- Blast with turkey baster into a white tray
- Remove plug if practical and re-mount
- Scrape/brush suspicious spots underwater
- Rinse in clean saltwater (separate container)
Dip + quarantine checklist
- Prepare dip + two rinse containers
- Measure dose and use a timer (no guessing)
- Agitate gently and baste crevices
- Rinse thoroughly
- Quarantine 4–6 weeks with weekly night checks
- Re-dip on a schedule to break egg cycles (as needed)
Ongoing prevention habits
- Don’t transfer bag water into your tank
- Keep QT tools separate from display tools
- Log new additions and observations
- Act early on “one pest,” not later on “many pests”
FAQ: Preventing pests in a reef aquarium
Do coral dips kill all pests and eggs?
No. Many dips can reduce mobile pests, but eggs often survive. That’s why inspection, mechanical removal, and quarantine are so important.
How long should I quarantine new corals before adding them?
A practical beginner range is 4–6 weeks. It gives time for eggs to hatch and for you to spot nocturnal or slow-building issues.
What are the most common hitchhikers on coral frags?
Common hitchhikers include aiptasia/majano, flatworms, nudibranchs and their eggs, vermetid snails, and nuisance algae like bubble algae or bryopsis.
Can I prevent aiptasia from entering my reef tank?
You can’t guarantee it, but you can reduce risk a lot by:
- Removing frag plugs when possible
- Inspecting and quarantining corals
- Avoiding water transfer from store bags
- Treating the first tiny polyp immediately
Should I remove the frag plug to avoid pests?
Often, yes—if the coral can be separated safely. Frag plugs are a common hiding place for eggs, algae, and aiptasia. If removal would damage the coral, quarantine and inspect the plug closely instead.
What is the safest beginner coral quarantine setup?
A small dedicated tank/container with heater, flow, basic light, frag rack, and stable saltwater (about 34–35 ppt, 24–26°C, and steady dKH) is a safe, beginner-friendly start.
Call to action
If you want a calmer, more pest-resistant reef, make your process consistent: buy carefully → inspect → clean → dip → quarantine. Track each step in Reef Buddy so you don’t miss re-dips or QT milestones, and so you can compare photos over time. If you’re unsure what you’re seeing, log it and bring the pictures—Shrimpy can help you turn observations into a simple next step.