Substrate question

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My Reef tank has been running for about a year and a half now. The Live Rock is 3/4 purple, No algea issues, however I'm having a really hard time keeping my sand clean. When I set the aquarium up, I used about 3" of some fine live reef sand. It's a 72 gallon with a korela 4 & 2. The flow is good.

Over the course of a year I've ran into algea outbreaks, ect..but now my sand seems to be full of dark brown and some purple particles which have literally changed the colour in some areas.

I try to siphon the Diatoms out weekly, but it just doesn't have that nice "white sand beach" colour anymore.

I see some reefers go bare bottom on their tanks, and others have flawless sand or crushed coral with no issues of discolouration. What's the secret? Do you replace the sand after awhile? What seems to be the best substrate?