Reefing Woes… Troubleshooting with Signature Analysis

by | Aug 11, 2022 | Opinion, Reef | 0 comments

Many reefers (beginners and veterans alike) will encounter setbacks that are inherent in this hobby. In order to find a correct path forward you must learn how to quickly identify and define the problems. If you don’t, you may be wasting precious time and possibly put your livestock at risk.  We all have to learn how to break down the components of our systems, drill down to more specific resources quicker, and ask the right questions. This problem solving process is defined as “signature analysis”. Understanding your system and all potential issues ahead of time prior to an actual event will save you stress and frustration in the long term.

Understand Your System

Understand the principles of operation of each piece of hardware and how it is supposed to work. Properly scheduled maintenance and cleaning is the best way to ensure proper operation.  Identify and create a list of symptoms that indicate when a piece of equipment is starting to fail or not perform at its peak.

Research all the requirements and behaviors of all the livestock you have.  The simplest reference is to take a picture of the organism when it’s in it’s best state of health and associate it with a complete water parameter signature.

A good reference snapshot of your system should include the following for each major event or fixed interval.

  • Full Tank Shot at various times of the day (Morning, Peak daylight, Night)
    • To understand coral coral poly extension behaviors which is a sign of good health

  • Individual closeup snapshots or video of each major organism
  • Basic Water Parameter Record: (Temperature, Salinity, pH, Alkalinity, Calcium, Magnesium, Nitrate, Phosphate)
  • ICP test sample taken from the same time frame since this will include some Major and Minor trace elements.
  • Notes of the current maintenance activities recently completed and things that need to be done.

The key is collecting enough data to determine patterns and trends you can attribute to a problem you are experiencing. Everyone’s system is unique so there are no “one size fits all” solution. This practice will help you sort through the tool box of internet information to apply working solutions.

I keep a running online log of my system and ICP test results on my personal website. The basic water parameters are recorded on my Neptune Apex Fusion, Coral Vue Hydros Controller, Dr. Bridge KH Guardian, and Reef Kinetics ReefBot test logs that are plottable on graphs for easy viewing of trends.


The system profile could be broken down in a more simplified manner. Here is a list, though not all-inclusive, of some of the most basic items.

  • Hardware
    • Tank / Sump (Total Water Volume defines level of stability)
    • Equipment (mechanical, chemical, and biological filtration, skimmers, pumps/wavemakers, heaters, lighting, controllers, ATO, etc.)
      • Create a maintenance check list related to each piece of equipment and intervals
    • Specific settings and configurations used. (Lighting spectrums and schedules, Wavemaker programs, Feeding regiment, etc.)
      • Document and back up settings just in case it needs to be restored
  • Livestock Inventory Database and Health
    • Fish
      • Proper habitat
        • Hiding places, swim space, feeding intervals etc.
      • Disease/Parasites (ich, uronema, brooklynella, flukes, fungus, etc.)
        • Use of a properly sized & set up UV Sterilizer to minimize algae spores, bacteria and viruses is beneficial.
        • Include natural predators for parasites as part of your stocking list. (i.e. Blue Streak Cleaner wrasses, Neon gobies, cleaner shrimp, etc.)
      • Nutrition (Hole in Head and Lateral Line Disease, etc.)
        • Ensure a mixed diet of ocean-sourced food items and feed based on their metabolic needs.
    • Corals
      • Proper placement for flow and lighting
      • Disease/Parasites (slow tissue necrosis, rapid tissue necrosis, brown jelly, bacterial infection, Acropora eating red bugs, Montipora Eating Nudibranchs, flatworms, etc.)
        • Always include natural predators for parasites as part of your stocking list. (certain Halichoeres wrasses, 6 line wrasses, etc.)
      • Nutrition (Nutrients & Trace elements in water column, proteins/amino acids, etc.)
    • Invertebrates
      • Disease/Parasites (Pyramid snails and pinched mantel disease = Perkinsus marinus on Tridacna Clams, etc.)
      • Nutrition (Nutrients & Trace elements in water column, proteins/amino acids, etc.)
  • Environmentals
    • Proper habitat aquascape for livestock
    • Proper amount of biological media /substrate (media, rock, sand, bare bottom)
    • Proper flow and circulation (no dead spots)
    • Proper lighting spectrum and intensity for the specific livestock (PAR, PUR, Photoperiod, DLI)
    • Basic Water Parameter stability (Salinity, Temperature, pH, Alkalinity, Calcium, Magnesium)
    • Basic Nutrient Balance (Nitrate : Phosphate ratio and range at a particular system maturity)
      • Related Problems:
        • Ultra Low Nutrients- Dinoflagellates, pale coloration of corals
          • Path: Reduce Denitrification and filtering efficiency, limit skimmer, increase feeding slightly, dosing nitrates and/or phosphates
        • High Nutrients- Diatoms (silicates present), Cyanobacteria, Algae, coral colors ‘Browning out’, Poor calcification of stony corals
          • Path: Use quality source water, limit bio-load and feeding, proper export methods chosen (water change, mechanical, chemical and biological filtration)
          • My personal choices for controlling Nutrients are simply just using web filters and properly tuned/maintained skimmers.
          • Algae turf scrubbers, refugiums and carbon dosing via Biopellet reactors work great though these require some level of tuning. These methods can be too efficient or if you are limited in space for this extra equipment.
    • Major and Minor Trace Element Replenishment
      • Some corals will start receding or not extend if certain trace elements are lacking.
      • ICP/Mass Spectroscopy testing is the best way to monitor for these elements to attempt to achieve balance
  • Signs of System Maturity
    • Development of micro fauna (copepods, amphipods, mysid shrimps, micro stars, etc.)
    • Existence of  filter feeders (sponges, feather dusters, mollusks, etc.)
    • Nutrient consumption levels are balanced and showing consistent growth and requiring increases in supplementation.


This may sound like a lot of work but it will pay off when completed.

  • Going through the process will familiarize you with your system in both good vs. bad states, as system matures and bioload changes.
  • Increase the understanding of various issues that may arise in each category ahead of time.
  • Develop a checklist of all the necessary medicines and supplements you may need to respond to properly identified problems.
  • Ellery Wong

    Ellery is a mechanical systems engineer at a Fortune 500 technology company. He has automation experience in the automotive, appliance, printing and robotics industries as a product development professional but also has over 35 years of saltwater aquarium experience as a hobbyist. He currently maintains a 9 tank / 540 gallon SPS/LPS/Mixed systems. DIY is his forte!


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