The aim of the study was to research the correlation of the level of PUFA (polyunsaturated fatty acids), PUFA-3, PUFA-6, EPA (eicosapentaenoic acid), DHA (docosahexaenoic acid), CLA (conjugated linoleic acids), MUFA (monounsaturated fatty acids), MUFA+PUFA and the proportion of PUFA-6/PUFA-3 in the profile of higher fatty acids of carp meat in the second year of life to the respective fractions in the HFA (higher fatty acids) profile of zooplankton in ponds fertilized using various doses of cow and sheep dung. It was found that the content of PUFA-3, EPA, PUFA-6 and PUFA depended on the increase of the content of these fractions in the HFA profile of zooplankton. The content of DHA and MUFA fractions depended on water temperature: the content of the first of the fractions dropped with a temperature increase, whilst the content of the second fraction increased. The variations in PUFA-6/3 proportions and PUFA + MUFA content in the HFA profile were seasonal in character: these values were always higher in the autumn than in the spring. The high fertility of the breeding environment of carp ponds, combined with a moderate density of stocking material, had a positive impact for consumers on the HFA profile of carp meat bred in a 2-year cycle.