Is this Safe (Modified Rock Cooking) to Deal with Past Algae/Cyana Problems


New member
So my 90 Gal Soft/LPS Mix tank (Glass Bottom) is going Fallow for next couple of months.

This all started since about a couple of weeks ago. All my fish died from a disease. Started with a new un-quarantined fish. Lesson learned!! That's a separate thread, now closed.

So having to tear down tank to retrieve dead fish (yeah, found last fish, under LAST ROCK taken out).....

I really want to take the opportunity to deal with a past re-occurring Algae/Cyano problem. (before starting my tank up again with Fish)

Sure, I'll be making adjustments, with Circulation, adding an Algae scrubber, and a refugium in sump. Something I've always wanted to do anyway.

However I'm pretty sure, my 15 year old nutrient infused rock was also part of the issue.

So with all rocks scrubbed, rinsed, scrubbed, rinsed. Rocks only are back in my tank (arrange for maximum circulation flow thru). All circulation powerhead pumps on max, including the Gyre (All running in swish swash cycles). (So powerful, this would not be idea for fish or corals, but good for a fallow period rock scrubbing).

All Corals are in Sump, and 2nd temporary holding tank.

I could properly cook my rock, and I still may. However reaching out for feedback about my modified rock/tank clean up approach (steps below).

1) My tank is now fishless, so nutrients are dropping (Skimmer still running[less&less each day]
2) I'm doing weekly small Carbon Changes to keep things fresh)
3) I put a light into my sump to keep corals alive. Plus this could be drawing the Algae to the sump (like a scrubber)
4) No lights on tank, and took a step further. Wrapped tank in BLACK Garbage bags, to shut off all light. (not sure how, long, but watching the little algae I missed. (To ensure it all dies with no light)
5) Am dosing daily Coral Snow, to help remove waste via skimmer.
6) Adding a 3 mls of Zeo Bak (Every other day or so), which I was doing before, trying to treat Cyano.
7) Planning on adding as recommended, some live brine shrimp, and copepods every so often to keep bacterial alive in the tank system. (or is this dangerous as they take over, with no predators)
8) I'll be feeding corals directly, and moving back and forth between sump and holding tank. (Rather than feeding nutrients into the whole system).

9) As I get close to the end of the fallow period, I'll clean the rocks again, and put back in final configuration. Put corals back, and slowly introduce fish. Expecting mini cycles.
10) New setup will have an aglae scrubber, refugium, and rock setup with max inner tank circulation.

So I believe the steps above should drastically reduce the nutrients in my rocks. Plus modifications mentioned, for a possible less algae/cyano problem free future.

I also expect the coralline on my rocks to die off from no lighting. I'm fine with that. ** Also Glass bottom tank, so no worries about any live sand **

This is not a full rock cooking, but a lite version of the process.

Also. Should I consider going back to sand bottom, which I stopped about a decade ago? Or will the new refugium addition with sand, be a good enough fix for this next restart.

(Hoping for less algae, and Cyano problems this time. None is the target/goal).

Any feedback about this rock cleanup approach? Any Additional recommendations? Is this a waste of time (can't really be)? Could this (tank-reverse) be harmful to my corals in the sump? (All Soft & LPS).

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New member
I honestly don't understand how this would remove any more nutrients from your rocks than just running as normal. This would work OK if you were just trying to cycle your tank, but if you really want to remove phosphates that you believe are leaching from your rocks, you need to treat them with something like lanthanum chloride, which you must do in separate containers.

Also, all of that feeding your doing is just going to produce nitrates, it's not going to help with a phosphate problem.

Did you run nitrate and phosphate tests when you were having algae problems? What were the levels for those?


New member
To be honest. I never did any accurate Nitrate tests. Just a multi test strip, and all appeared fine. The Phosphate tests with Salifert kit, never registered any Phosphate (kit is expired).

I'll look into treating rocks with lanthanum chloride. Thanks for the tip.

However before I do.

Will also get new test kits:

For Nitrate (Salifert kit),
Phosphate (more accurate one). (Hanna?). However for Hanna there are two kinds. Phosphate and Phosphorus. (which is best?).


New member
Maybe others will have different experience, but I have never had my hanna register any phosphate (although their Alk checker is awesome). I started using the red sea kit for nitrate and phosphate (you can get both in a kit called "nuisance algae kit" or something similar) and they work really well.

If you really believe your rocks are leaching phosphate, "cooking" them is really the only way to remove it (or waiting for however long it takes in the actual tank). It's really best to know what you're dealing with before you start a bunch of different tasks to try and fix it.


Staff member
RC Mod
I had a really bad case of phosphated rock: I just ran GFO---a lot of it--- and it got it. There's no fast track, because the rock has to soak clean all the way to the core of the rock, and that just takes time. Rock does not get wet all the way inside easily, but over time, it does. Something to bind it permanently is a good thing (that's what granulated ferric oxide does) but time, time, time.


Active member
So.. I don't think your method of cooking the rocks will be effective. Most of the guides say to deprive them of sunlight entire, and of nutrients. That way everything on there has nothing left to eat and you are left with dead rock. you swirl them around and get all the sand and silt and dead stuff out. and continue doing that for about 2 months, with water changes. - This kills all algae on the rock.

It sounds like your system will still be getting nutrients so things are still going to be alive...

I'm not sure if light deprivation will be enough to destroy it entirely, part of the method is nutrient deprivation too.

I've had persistent hair algae in the past, even though phosphates and nitrates were 0.. I never tried a phosphate removal system though, not sure if that would help, I'd assume the phosphate/nitrate was being consumed by the hair algae and a phosphate reactor might grab it before the algae has a chance to? I dunno.


New member
Similar to what other posters have told you, the best strategy to rescue your tank from high nutrients would be to 1) black it out for a week or more. That'll kill the actively growing algae, but not take care of the nutrients; 2) Install a reactor and run High Capacity GFO in it. 3) With continued aggressive skimming, dose your tank with the appropriate amount of vinegar as described here.

If you want to test your progress with the carbon dosing and GFO, buy a Salifert nitrate test kit and a Hanna checker 713 Low-Range Phosphate Meter with an extra reagent pack - both are available from Bulk Reef Supply and others. Do not buy the Hanna Checker Ultra Low Range Phosphorus 764 test, though you may have some posters advise you to do so.

Bulk Reef Supply has their high capacity GFO on sale at the moment, btw. You can regenerate GFO to save some serious $$$ if you're willing to work with caustic solutions.

Edit: Discontinue the ZeoBak and the Coral Snow. There's lots of folks that like and use Korallen-Zucht ULNS products, but in your case, they're not appropriate, particularly because you're trying to recover a tank instead of maintaining a well-functioning one, and we don't fully know what's in KZ products - you potentially might be making things worse.


Premium Member
Do not buy the Hanna Checker Ultra Low Range Phosphorus 764 test, though you may have some posters advise you to do so.

Why not? I assume you are referencing the 736 ULR Phosphorus checker and not a 764 which is for nitrite. If that is the case I completely disagree.


New member
Why not? I assume you are referencing the 736 ULR Phosphorus checker and not a 764 which is for nitrite. If that is the case I completely disagree.

Yep, sorry, that was a typo. The ULR Phosphorus checker has some rather clear reagent problems that I didn't encounter with the 713. So much so that I sold the 736 after going through 3 lots of reagent packs that were problematic.


Premium Member
There have been bad batches as well as bad checkers as with all test kits. Here is my reasoning for disagreeing.

If a 736ULR reads 1ppb phosphorus (the lowest it can read other than 0) given the margin of error the actual number could be as high as .018ppm

If a 713 reads .01ppm phosphate (the lowest it can read other than 0) given the margin of error the number could actually be as high as .05ppm

While that may be fine in some cases I feel it is not adequate for accurate measurements in a reef. If my 736 shows 10 I know I am too high. The lowest registered number with error on the 713 is higher than I like to keep my tank so it is of no real use for me. I'd also like to point out I have made hundreds of tests between my two 736 checkers and the only botched results were from user error. I've had plenty of that.


New member
So, I'll put all my remaining corals from sump into the holding tank (ideal time to try out new Kessil 360W, that just arrived in mail today), and let the tank go dark, and nutrient free and long as possible. Maybe not all the way to fully dead rock, but enough to get a better fresh start.

I did add Reactor and am using RowaPhos. Plus regular carbon changes. Rocks should (SLOWLY) difuse their accumulation. Especailly with tank running max circulation.

Not really keen on any harsh chemical methods.

But I will get the best test kits, I can for Nitrate and Phosphates. Thank for everyone's input.

Just remembered, I should take out that Urchin that I left in the tank to scrub any algae left on rocks.

SO NO opinions with going SAND Bottom vs GLASS bottom for next startup? I switched from Sand a decade ago believing it was just another nutrient/phosphate trap (so maybe rocks did the soaking instead)
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New member
SO NO opinions with going SAND Bottom vs GLASS bottom for next startup? I switched from Sand a decade ago believing it was just another nutrient/phosphate trap (so maybe rocks did the soaking instead)[/QUOTE

I think it is a case of one person's biofilter is another's nutrient trap. There does not seem to be a right or wrong answer here. I like the look of a substrate, but if I was just growing out frags, substrate may not serve a purpose.


New member
Wally - With respect to tkeracer's and my disagreement over which phosphate meter, I'll simply note that this is a fairly fine point. Either of the Hanna Checkers will be far, far better than one of the "color chart" tests, which are simply too insensitive to be of much use for a reef tank. And it will be far better to have either checker than none if for no other reason to help you minimize GFO expenditure (it's pricey stuff).

By the way - your rock won't die under a short-term (a week or so) tank black-out and low-nutrient conditions. You may experience some loss of coralline algae, but this will be very temporary.

From the standpoint of regenerating your GFO - the harsh chemical you need to do this is sodium hydroxide (lye). You need to make a 1M solution, which is 40 grams in one liter of RODI. Approximately speaking, that's about 9 teaspoons per quart (the exact concentration isn't critical, just get it close). You simply make the NaOH (lye) solution from "pure lye" sold at home stores, put the GFO you wish to regenerate in a mason jar or other glass container, pour enough of the lye solution into the jar with the GFO to give you 2" of clear liquid over the GFO, stir it gently, and allow it to stand for several hours. Pour the lye solution off, and repeat the above addition/standing/pour off of the liquid for a total of 3 cycles. Then rinse the GFO with copious amounts of RODI.

The precaution you need to take with the lye solution is to wear black rubber mid-forearm-length janitor's gloves, and a pair of safety glasses to prevent a splash to your eye. Lye solutions don't make fumes, so you can do this at the kitchen sink, just don't get the lye solution on your skin. If you do, you've a few seconds to thoroughly rinse it off.
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New member
SO NO opinions with going SAND Bottom vs GLASS bottom for next startup? I switched from Sand a decade ago believing it was just another nutrient/phosphate trap (so maybe rocks did the soaking instead)

This is a controversial subject, and you'll get impassioned debate on both sides. I've run both (bare-bottom and sand-beds). I prefer sand beds because I like the look, and some types of animals that I keep require it. In my opinion, both types of tanks can be kept successfully; I've a nano 20g high that's been running with a 2" sand-bed for 11 years now, and while it has some degree of algae in it, it's not a plague or something that over-grows my corals.

Read up on the vinegar dosing methodology for reducing/eliminating nitrate. With a lot of algae in your tank, you may actually test 0 ppm for nitrate and phosphate because the algae is consuming it as rapidly as it's produced. But it's still there, and feeding the algae, so reducing the flux of these nutrients by running GFO and carbon-dosing will be important to prevent a return of the algae once you've killed a lot of it off with blacking out the tank and returned to a normal photoperiod.


Premium Member
There was a kick years ago to go with a deep sand bed. And those while they can be properly maintained are often a ticking time bomb.

I like to keep sand but keep it to about an inch.


New member
I just removed my sump, which is going to be cleaned.

Substituted a Rubbermaid bin, and put back skimmer, GFO reactor, and carbon.
Lid is going on tomorrow, so that full system will be darkened. Corals in holding tank, so the whole system will be nutrient free.

Peeked into the Dark Tank, all looks fine. Notice the only living thing left (the Urchin), is moving around like never before. Must be munching on Coraline, since Green Algae supply must be sparse. I'm fine with that, since this will open up the pores in the LiveRock.

I'll probably go with the Hanna Kit for Phosphate testing. I have a hard time reading the color wheel kits.
Still deciding on which Nitrate kit to go with. (Any recommendations).

So a good point was raised by "dkeller", which I was probably experiencing. I could never get a Phosphate reading with my Salifert kit (Clear white = 0ppm). I even had someone with a Hanna kit do a test (reading was really low)...Reason may have been the Algae was eating up the Phosphates, Nitrates and thus growing very fast. Such that kit was not picking up anything much left.

Will read up on Vinegar dosing, to be ready for this option when tank starts up again.

And lastly. Going to stay Glass Bottom, or very thin layer of sand. (Yes I love sand look too). Got sand in my other SPS only tank. Sparkling white always, since I have a Diamondback "SandShifting" goby.

Thanks for everyone's input, each perspective give me confidence for an Algae Free future.

(Will post pics of the refreshed tank, when I crack open the Dark Seal). I have before shots. And will take shots every week or so.
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New member
Still deciding on which Nitrate kit to go with. (Any recommendations).

An awful lot of us like Salifert for nitrate. Some prefer Red Sea. Almost no one prefers API, if that helps any.

Will read up on Vinegar dosing, to be ready for this option when tank starts up again.

Actually, I'd recommend you start with this while you've got the tank blacked out. There will presumably be a spike in nitrates from (at least) the decaying algae, and the vinegar dosing method for controlling nitrates depends on a slow ramping up of the dose to establish and encourage denitrifying bacteria colonies in your rock, and bacterial growth in general. Aggressive wet-skimming during this process will help you remove both nitrate and phosphate, since the bacteria you remove by skimming have consumed both nitrogen and phosphorus to grow.


New member
Here is an update after tearing tank down, and going TOTALLY DARK.

Photo of tank after 2 weeks of complete Darkness, no nutrients.
Continuing with skimming, GFO, Carbon media,
and ZeoVit Coral Snow dosing (Which is aiding in removing of Nutients).

Test of Phosphate=0ppm (Using Hanna), Nitrate=5ppm (Using Salifert)

Planning to reconstruct with better Algae control next time. (I'm Hesitant about Vinegar Dosing, due to what I've read so far).
Certain planning to construct an Algae scrubber device in the new sump.

Have lifted DARK top cover today. Will continue side covers for another week.

Picture is with no lighting, just camera flash so it hard to tell how VERY well rocks look.
[WEEK 2] Sparkling clean rocks (Zero Algae, Cyano). Some Coraline loss.

[BEFORE few weeks earlier] Tank with Algae/Cyano Problems (During better algae times. Was much worse!!)]

[OLD GLASS SUMP Torn Down and Cleaned][/


(Glass Sump replaced with Rubbermaid Sump (keeper)...Way quieter!!!) Work in progress for final Tank Reconstruct.

[Corals resting well in Holding tank/future Frag tank..... made from ABOVE OLD sump.]

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New member

So I have restarted the tank. Lights back on and some corals back in.

Corals are doing really well in the Hair Algae free tank.

I started Vinegar dosing about 2 weeks ago as per POST. 15 ml each day (100G tank) (has that been too aggressive? Should I cut back, or keep going till I reach 45ml max slowly?)

I did start feeding Corals a bit, but have stopped, since I notice algae coming back all over rocks. I assume this is part of a re-start cycle (algae cycle).a
I even see bubble algae starting, so added an Emerald Crab, who is quite busy now.

I stopped feeding corals since want to wait till Nitrate is down to zero.

Should I be concerned? Is algae bloom going to go away?

Should I be careful and slowing increase light time? I've gone back to 3 hours main lights (Kessil 10%). 8 hours accent lighting. (2x T5 Actnics)

Here is what tank looks like now.


Here is the algae that is starting back.



Also, it was mentioned that with Vinegar dosing, I may see white bacteria growth. I see white specs all over rocks. Is this the bacteria? (I assume this is good)


Any advice?
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New member
Dude, honestly its a battle we all will fight, I had algae issues for a long time in my old 72 gallon, finally went away, what I began to do, was simply add a GFO reactor, dose Mg and siphon off any detritus I saw. I bought an amazing cuc too. Look into a fromia sp sea star. not to popular in the aquarium trade but ive got one in my 20 and three in my 150. Red with black tips. They also eat cyno, but unlike seahares, who are known to eat cyno and algae only, these guys eat detritus and other food stuffs. Very slow movers. But if they die they do not emit that poison that sea hares do. Its a perk. There are these poly filters that remove everything from the water column, excess organics, ammonia, nitrite, nitrate phosphate, you may want to consider that until your issue goes away. I know when I added mine, my protein skimmer went NUTS!! As far as sand bottom, I like it because I feel it does aid in general biodiversity to your tank, Maybe not the easiest to clean. But no more than an inch and a half you shouldn't be facing any issues with buildup as long as you have no stagnant areas. cyno is stubborn and will just take time, but I would definitely run GFO, the Poly pad and make sure flow is good. do you have a refugium? that could help for sure. I grew calurpa and still do in my 20 and I pulled softball size portions out weekly. Good source of nutrient removal. I don't like dosing things like vinigar or vodka because they are not stable and will alter your water chemistry. Mg is a tad risky but doesn't cause a huge swing plus its hard to overdose on.