Dinoflagellates: Understand, Prevent & Treat – François Neo’s Complete Guide
Introduction
Hey everyone, Francois Neo here!
Today, we dive into the microscopic (and sometimes maddening) world of dinoflagellates. These are unicellular protists — some photosynthetic, others not — that in reef aquariums can bloom, form brownish-viscous films, alter water tint, or weaken corals.
In this post I’ll cover what dinoflagellates are, why and how they appear, the best prevention strategies, and effective treatment methods. As usual, I’ll share my own tips + trusted products — especially from ASF — to help your tank stay stable and beautiful.
Chapter 1: Understanding Dinoflagellates — Origins & Mechanisms
What are dinoflagellates?
- Protists with one or two flagella, free-living in water column or attached to surfaces.
- Many are photosynthetic; some are mixotrophic or heterotrophic.
Why are they a problem?
- Reduced light penetration for corals.
- Mucus or film that smothers live rock or coral surfaces.
- Some species may release toxins or otherwise stress fish/corals.
Conditions that favor proliferation
- Nutrient levels too low, notably nitrates and phosphates undetectable.
- Poor water circulation, dead zones.
- Organic waste build-up: food remnants, mucus, decaying matter.
- Miscalibrated lighting: duration, spectrum, intensity.
- Weak microbiome or little biological competition (algae, beneficial bacteria, microfauna).
Chapter 2: Prevention — Setting Up for Success
Here are the actions I use in my tanks, inspired by community feedback and literature:
| Action | What I Do / Recommend |
|---|---|
| Maintain measurable nutrients | Aim for 5-10 ppm nitrate and a detectable phosphorus level (~0.02-0.1 ppm depending on tank) — avoid absolute zero. |
| Ensure good circulation | Use wave makers / power heads, avoid dead spots behind rock work, ensure water flow reaches all zones. |
| Clean regularly | Remove organic debris, siphon sand, brush off films or visible mucus. |
| Biological diversity | Use live rock/sand, maintain microfauna (copepods etc.), sustain macro/micro algae for natural competition. |
| Balanced lighting | Proper duration and spectrum to favor coral growth without feeding algae/dinos. |
| Frequent monitoring | Test nitrates, phosphates, pH, alkalinity, etc. Observe suspect samples under microscope if needed. |
Chapter 3: Treating an Active Outbreak — Francois Neo, Protocol
When you're already dealing with a dinoflagellate bloom, here’s the protocol I use, combining mechanical, chemical, biological approaches with ASF products:
Step A: Precise Diagnosis
Take sample (mucus/film), examine under a microscope to confirm dinoflagellates, identify whether free-swimming or fixed.
Identify affected area(s): sand, live rock, decorations, glass.
Step B: Adjust Water Parameters
Gradually raise nitrates and phosphates if they are undetectable.
Stabilize alkalinity (KH), monitor pH for swings.
Check salinity, temperature, oxygenation, reduce stressors.
Step C: Mechanical Removal & Blackout
Daily siphoning of visible mats or films from sand/rock.
Implement a blackout (full or partial): 3–4 days with main lights off (but refugium might stay lit). Monitor temperature, oxygen.
Clean protein skimmer, mechanical filters, remove visible slime.
Step D: Boost Competition & Restore Microbiome
Add beneficial bacteria / probiotics.
Introduce microfauna (copepods, etc.).
Maintain or grow macro-algae in refugium to absorb nutrients and serve as natural competitor.
Step E: Use of UV Sterilization (if applicable)
Use a properly sized UV sterilizer with correct flow rate to ensure contact time.
Position in system (often in sump) so water passes through UV.
Maintain quartz sleeve, replace bulbs as needed.
Step F: ASF aquarium System Products to Incorporate
Here are ASF items I use or recommend, and how to integrate them in the treatment protocol:
| ASF Product | Role in Treatment |
|---|---|
| ASF Reef Shots Reef Bacteria Food | Helps restore beneficial bacterial populations, improve competition against dinos, especially after cleaning / blackout. |
| ASF Reef Shots Reef Elements / Calcium / Magnesium / Strontium Shots | To stabilize essential reef elements, prevent weakness in corals during stress periods. |
| ASF Reef Shots Probiotics | To strengthen the microbiome, help crowd out unwanted organisms. |
| ASF MX / NewJet DC Pumps | Increase water circulation, reduce dead zones, help distribute supplements and improve UV effectiveness. |
Step G: Follow-Up & Prevent Relapse
Frequent testing (twice a week at least during recovery phase) of nitrates, phosphates, pH, alkalinity.
Slowly restore lighting (post-blackout), avoid sudden jumps.
Keep supplementing (e.g. with Reef Shots) for essential trace elements.
Ensure a strong diversity of life: microfauna, macro-algae, live rock/sand, etc.
Chapter 4: Common Mistakes to Avoid
Changing too many parameters at once (nutrients, lighting, filtration) without monitoring can cause coral stress.
Using harsh chemicals without understanding species / compatibility.
Neglecting stability: large swings in temperature, salinity, pH.
Skipping follow-up; many outbreaks come back because maintenance and vigilance drop once visible symptoms fade.
Conclusion
Dinoflagellates—despite their tricky reputation—are far from unbeatable.
They appear when your aquarium’s balance is disrupted: nutrients too low, a weak microbiome, poor water movement, and similar issues. But with a careful diagnosis, a structured treatment plan, reliable products (including ASF), and consistent follow-up, you can not only eliminate them but also build a reef aquarium that’s vibrant with life, color, and long-term stability.
If you ever feel stuck, share the type of dinos, your tank conditions, equipment, and budget—I’ll gladly help you fine-tune the protocol for your specific situation.
Use code NEO15 for 15% off ASF Reef Shots!
See you soon on the blog, Instagram,
Francois Neo