Hello there, new to this site, perusing the net as it's late at night.
I have had a similar problem in my 125 gallon tank. Heres the scenario and how it played out.
I have 12 fish, low bio load, 180lbs live, highly porous fiji rock. Up until I fixed the problem, I was using regular unfiltered tap water for salt mix as well as top off. The substrate was crushed aragonite, around 3" in some places. I use a canister filter (magnum 350), an Emperor 400 hang-on, and I was using a sump wet/dry with a ton of bioballs. My salinity was in the 1.024-1.030ish area, temperature around 78-82 (fluctuating temp inside the house.. its hella hot). My filter medias are/were 20 gallon high sump filled with bioballs, emperor 400 with 2 flossiies and 2 carbon pads, and the canister is used to deploy carbon bags and extra flow. I have 5 maxi-jet 1200 powerheads strategically placed for maximum flow, just one single dead spot.
I test my water every day. All of my levels were fine except for the nitrates, which were reading 40ppm+. I had an insane bloom of algae, so I was primarily battling that off. My first course of action was to try and figure out why the algae was going nuts. I tossed in some Phos-Zorb, which is garbage. I replaced that with PhosGuard by seachem, to take away that food source. I also started topping off with distilled water from Meijer. Algae growth still took off over the course of 2 weeks. My nitrates were a steady 40ppm. I decided to take out the bioballs, for fear of overnitrifying bacteria, and began to convert my sump into a fuge. (still waiting on chaeto) Took out my LR and scrubbed/plucked the algae off, and gave them a 4 hour freshwater bath. Algae was still relentless. I replaced all four of my 72" VHO 50/50 // White // blue actinic lights, and added a closed loop manifold. I even performed two 55gallon water changes with RO water over the course of a month. At this point I was stumped. I had tried just about everything, until I thought about it. What was I missing, right before my very eyes? My gravel bed! At 3" depth, I had over 200lbs of aragonite in my tank, along with the highly porous LR. The beneficial bacteria in my tank was now detrimental. It took me a lot of patience and 14 hours of work, but I scooped out all of my aragonite, and replaced it with a soft bed of 40 pounds of brand new Oolitic sand. After each step, my nitrates remained a strong 40ppm immediately after, and a week after implementation, but when I removed my gravel bed, voila 10ppm reading. Its still not where I wanted it to be but it is a whole lot better than it was. My tank Probably has about 2 months worth of 55gallon-every-two-weeks water changes before It is cycled into brand new RO/DI-S (Maxxima Deluxe) water, so by then I expect to have pristine water.
So heres some tips in summary.
-Check the levels every day. (Hagen Master test kit)
-Try to keep the temp at 78d
-strict lighting on timers
-increase water flow (I have 2575gph approx) or 2x the amount needed
-I added carbon, phosphate, and silicate removing compounds. (I HIGHLY reccommend **** Boyd's Chemi-Pure)
-Regular water changes, with 1 gallon a day in general
-Use turkey baster to blow off detritus from rock and substrate
-Buy a brine shrimp net, and RINSE any frozen prepared foods in the net... The juices are like nitrofuel for bad stuff
-I tend to try and limit my bio nitrification to only the rocks, as that is what works for me. Others swear by the dynamic sandbed, but ive only had trouble with it. Instead, I say provide a suitable refugium with either chaetomorphia or caulerpa (chaeto has the benefit of abosrbing nutrients as well as caulerpa, but when the caulerpa dies, it releases the harmful nutrients...so ive heard.) A refugium will do the same thing as beneficial bacteria, but will add dissolved oxygen instead of removing it as bacteria does. Plus you get growth of little yummies for your fish.
-Add in little sand sifters to stir up the substrate and some for algae control. (brittle star, blue leg hermit crab, scarlet hermit, nassaurius snail, Trochus snail, lawnmower blenny, a sea hare slug... they pay off. One turbo snail of 1" size eats a TON of algae, more than you would think.)
-Did I mention use **** boyd's chemi-pure?
-Feed with a turkey baster so as to not contaminate the water with your hands. Ammonia and Phosphorous can be introduced to the tank from a bathroom break or a mcdonalds chicken sandwich (c'mon, get it? the commercial? n'mind)
-Get a Maxxima RO/DI-S system, itll turn you on.
-Theres conflicting reports on using a skimmer, I use one as it makes me feel good inside when I wash out a cup of skimmate. Feels like some equipment is actually working. Plus I have something to fiddle with.
Ok I cant think of anything else right now, its 2:30 in the AM. Hope my post helps some =D
Adam