Nitrates are introduced from the process of artificial biological filtration (sponge filters, bioballs, trickle filters, u/g filters, hang on filters, etc) breaking down waste. I can not tell from your pictures what type of filtration you are running, but it looks like you are very close to an easy solution to this problem.
The most effective method of removal is live rock and sand, along with an efficient protein skimmer. You have a shortage of live rock, which could be easily and inexpensively fixed with an order of dry rock from Marco Rocks The finest aquarium rock available, base rock, live rock, reef rock, marco rock, reef tank saltwater fish, live corals, Marco rocks, Fiji live rock, Tonga Live rock
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Live rock and sand will harbor bacteria that are denitriying bacteria, meaning they convert nitrates to nitrogen gas, which leaves the system naturally. These types of bacteria can not live in traditional biomedia filters, such as those named above. For this reason, live rock and sand are the most efficient method of filtration for a marine aquarium. To compliment these, adding a protein skimmer to remove organic waste PRIOR to the waste being broken down into ammonia, will greatly improve the efficiency and stability of your system.
What sort of filtration are you running currently?