The primary objective of this study is to investigate the effects of Zinc toxicity when fishes are exposed in a controlled environment using two-dimensional correlation spectral analysis. This analysis is superior as subtle spectral changes induced by an external perturbation are not readily noticeable in conventional one-dimensional spectra. A higher decrease in protein and carbohydrates and a lesser decrease in lipids (20%–28%) against the control sample occurs due to Zn toxicity. The lowest value of the bioconcentration factor for Zn shows carbohydrate utilization, which was resolved well in our two-dimensional spectral analysis. Synchronous maps show the predominant changes in protein (1668 cm−1), phospholipids (1771 cm−1), and fatty acids (1707 cm−1). The asynchronous two-dimensional spectra show alteration in phosphodiester stretching of glycogen followed by Amide I. In addition, we explored the importance of principal component analysis coupled two-dimensional spectra analysis which shows weak amide III protein changes. The hetero asynchronous shows well-resolved cross peaks of +(1047, 1389), resulting in improved resolution. The study helps in understanding biomolecular changes of muscle tissues of G. affinis under Zn toxicity using two-dimensional correlation infrared spectral analysis.