Biogen elements that enter the water in large quantities are one of the main pollutants in the aquatic environment. They lead both to eutrophication of the reservoir and a decrease in the viability of young fish, acting as toxin. The energy enzyme activity (lactate dehydrogenase and succinate dehydrogenase), nitrogen (glutamate dehydrogenase) metabolism, dephosphorylation processes, and immune protection (by alkaline phosphatase activity) under the long-term action of ammonium nitrogen and phosphorus phosphates was studied. The biological object of research were 30–45 day common carp juveniles (Cyprinus carpio L.). According to our results, the peculiarities of the adaptive reactions of young carp to the action of these compounds have been established. We revealed, that under the loading of ammonium nitrogen, the activity of the processes of anaerobic digestion of energy-intensive complex increases directly in the organs of neutralization and excretion of nitrogenous compounds, namely in the gills. In general, the body of the carp due to these actions reduces the total energy consumption for maximum survival in these environmental conditions. We registered, that under the influence of elevated concentrations of phosphorus phosphates, oxidation of biogen elements to the body's energy needs in the presence of oxygen was observed. The processes of immune defense and dephosphorylation, for which LPh is responsible, also the detoxification, the excretion of nitrogenous substances from the body of carp (GDG) occurred differently depending on the chemical nature of the toxin. Thus, under the influence of ammonium nitrogen there was an increase in the activity of LPh in the highest concentrations of the toxin, and the activity of GDG decreased to reduce the production of ammonia, to avoid endogenous intoxication. Through these load of potassium monophosphate, the rise in the activity of immune defense processes and the involvement of ammonia in the cycle of tricarboxylic acids due to reamination to the energy supply of the processes of counteracting the weak but chronic toxic effects of orthophosphate ion. Under the load of ammonium chloride was observed not only the use of “traditional” energy substrates - glycogen and lipids, as well as proteins, which indicates the high toxicity of this compound for the body of young carp. Through the action of orthophosphate ion, the active use of lipids and even the activation of gluconeogenesis at maximum concentrations, as a reaction to weak long-term chemical stress.