Organophosphates (OPs), commonly used pesticides to increase agricultural production with minimal labor efforts, unknowingly affect non-target animals. Amongst OPs, malathion (MAL) is a neuro- and immunotoxic and widely used. This investigation aimed to understand the multiple physiological responses in common carp exposed to MAL. In this study, acute toxicity test showed 6.75 mg/L as LC50 in 96 h, following which, a separate sublethal toxicity test was conducted (28 d), having environmentally realistic (2.618 μg/L) and higher concentrations (0.675 & 1.35 mg/L). In higher exposures, selected transcripts such as acetylcholinesterase (Ache) and component complement-3 (c3) levels significantly decreased. While, hematological parameters [(total erythrocytes (TEC), hemoglobin (Hb), hematocrit (Ht), Mean Corpuscular Hemoglobin (MCH), and Mean Cell Hemoglobin Concentration (MCHC)] reduced with an increase in MAL levels except for total leucocytes (TEC), which increased significantly (P<0.05). Further, histomorphology of the brain revealed disparaging alterations such as degenerated neurons, pyknosis, vacuolization, increased fibrous components, and focal necrosis with MAL exposure. Whereas gills showed hyperplasia, telangiectasia, and fused lamellae, and kidney revealed damaged glomeruli, increased lumen, and exudates. While the liver exhibited a shrunken central vein, thickened bile duct, and dilated portal vein, with exposure. Collectively, the study revealed that MAL is neuro- and immuno-toxic and damages the microarchitecture of the tissues. The non-judicious application of MAL leads to harmful effects, hence, usage should be monitored regularly.