Manganese (Mn) is an essential element for humans and animals including, fish. It is a still poorly studied in aquatic organisms, where it can be noticeably useful for dietary components and also found pollutant in aquatic environment at high concentrations. On the above information, an experiment was delineated to determine the lethal concentration of manganese (Mn) and manganese nanoparticles (Mn-NPs) alone and with high temperature (34 °C) and its effect on various biochemical markers inPangasianodon hypophthalmus. The median lethal concentration (96-LC50) of Mn alone (111.75 mg L−1) and along with high temperature (110.76 mg L−1), Mn-NPs alone (93.81 mg L−1) and with high temperature (34 °C) (92.39 mg L−1) was determined inP. hypophthalmus. The length and weight of the fish were 6.32 ± 0.23 cm and 7.57 ± 1.35 g. The present investigation used five hundred forty-six fish, including range finding (216 fish) and definitive test (330 fish). The acute definitive doses were applied to assess the effect of oxidative stress, glycolytic biomarkers, protein biomarkers, fish immunity, neurotransmitter, energy level, stress hormone and histopathology. Oxidative stress (catalase, superoxide dismutase, glutathione-s-transferase and glutathione peroxidase), stress biomarkers (lipid peroxidation, cortisol, heat shock protein, and blood glucose), lactate and malate dehydrogenase, alanine and aspartate aminotransferase, a neurotransmitter, glucose-6-phosphate dehydrogenase (G6PDH), ATPase, immune system biomarkers (NBT, total protein, albumin, globulin and A:G ratio) were altered with exposure to Mn and Mn-NPs. The histopathology of the liver and gill were also changed due to exposure to Mn and Mn-NPs. The bioaccumulation of Mn in the liver, gill, kidney, brain and muscle tissues, and experimental water at different intervals of 24, 48, 72 and 96 h were determined. Based on the present results, it is strongly suggested that Mn and Mn-NPs exposure alone and with high temperature (34 °C) enhanced toxicity and altered biochemical and morphological attributes. This study also suggested that essential elements in both forms (inorganic and nano) at higher concentrations of Mn and Mn-NPs lead to pronounced deleterious alteration in cellular and metabolic activities and histopathology ofP. hypophthalmus.