Fresh water ecosystems have been contaminated alarmingly through a number of heavy metals. Lead is a purely toxic heavy metal widely used in different industries and causes serious damage to aquaculture species such as fish. The present work explores the toxic effects of lead on liver of fish Cirrhinus mrigala and the spectral and surface morphological changes in liver. Fourier transform infrared spectroscopy (FTIR), energy dispersive X-ray spectroscopy (EDX) and Optical absorbance are the currently used method of monitoring animal tissue and their components. The biochemical profile of liver was explored by FTIR, EDX and optical absorbance. The surface morphology of liver is studied by field emission scanning electron microscopy (FE-SEM). The present study gives a manifold confirmation on the alterations at cellular level after chronic exposure to lead.