Assessment of acute toxicity of magnetic nanogel (MNG) is crucial to conclude the safe applicable dose and to warrant its application in aquaculture. Therefore, the current study is a novel step to assess behavior, neuro-stress response, hepato-renal, oxidative, and histopathological variations produced by MNG’ acute toxicity in Clarias gariepinus. Two experiments were conducted: the first was a determination of the 96-h lethal concentration 50 (LC50) of MNG in C. gariepinus. Meanwhile, the second was an assessment of the toxicological impacts of three different concentrations of MNG in C. gariepinus following a 10-day exposure period and a subsequent 10-day depuration trial. One hundred and eighty fish were allotted to four groups exposed to 0, 1/10, 1/8, or 1/5 96-h LC50 of MNG. The outcomes exhibited that 96-h LC50 of MNG for C. gariepinus was 44 mg/L. The subjected group to MNG induced a concentration-dependent elevation in the serum values of cortisol, alanine transaminase, aspartate transaminase, urea, and creatinine following MNG exposure. Marked elevation in the oxidative stress indicators (catalase (CAT), glutathione S-transferase activity (GST), and superoxide dismutase (SOD)) was also evident. Meanwhile, the value of the neurological biomarker, acetylcholinesterase (AChE), was markedly reduced in a concentration-dependent way. These biochemical changes were complemented by pathological alterations in the hepato-renal architecture. Interestingly, in response to the 10-day depuration period, most of the tested parameters were eliminated in C. gariepinus exposed to 1/10 of LC50. Conclusively, MNG can induce numerous adverse effects only at higher doses (1/5 and 1/8 of LC50). Meanwhile, the lowest tested concentration of MNG (1/10 of LC50) was safe for application in aquaculture practices with only mild disruptions in the bio-indices. In addition, a retrieval period of 10 days was sufficient to renovate these alterations only in fish exposed to the same concentration.