You ned to study ...

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You ned to study physicochemical parameters like pH (for both effluent and influent) temp, color, DO, BOD, COD, TDS, TSS, TS, Chloride Sulphate, Oil & grease also. to understand cause of coloration. As you using allophanic filters, which helps to reduce the coloration of iron containing waste water. I guess, Iron is not the cause.