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This paper addresses the problem of controlling turbidity, dissolved oxygen, ammonium‐ion concentration, and water‐temperature to maintain the desired water quality in an intensive aquaculture plant. The research is carried out to fit into the present scenario of intensive aquaculture in India. The plant model along with uncertain parameters are derived using physical laws and the data acquired from an aquaculture pond in Assam, India. A pre‐compensated multi‐variable quantitative feedback theory (QFT)‐based fully populated robust matrix controller is proposed to mitigate the control challenge. A novel method is used to design the pre‐compensator to enhance the diagonal dominance of plant transfer function matrix. The desired robust stability, reference tracking, and sensitivity specifications are fulfilled by the proposed QFT‐based robust controller despite the parametric uncertainty. The effectiveness of the proposed method is validated through numerical simulation. A comparative study against a H∞$$ {H}_{\infty } $$ controller shows that the proposed controller strategy gives a satisfactory performance compared to it. [ABSTRACT FROM AUTHOR]