The present study aims to evaluate differences in the incorporation efficiency and the possible interactions among highly unsaturated fatty acids (HUFA) during enrichment and starvation of Artemia nauplii. Artemia franciscana nauplii were enriched with emulsions containing docosahexaenoic acid (DHA, 22:6 n−3), eicosapentaenoic acid (EPA, 20:5 n−3) or arachidonic acid (AA, 20:4 n−6) as sole HUFA or with different ratios of these HUFA during 24 h at 28°C and subsequently starved for 24 h at the same temperature. The comparison of HUFA incorporation efficiency when supplying the three HUFA separately showed a less efficient enrichment of DHA as compared to AA or EPA. DHA incorporation was always accompanied by an EPA increase, indicating the metabolic conversion of DHA to EPA by the nauplii during the enrichment process. When offering the HUFA together, we found no competitive interaction of EPA or of AA on DHA incorporation. Only in the case of the 97% (% total fatty acids) n−3 HUFA emulsion, some negative interference might have occurred between the HUFA, as it gave a lower incorporation of 22:6 n−3 and 20:5 n−3 than the emulsions with lower n−3 HUFA content. During the subsequent starvation of EPA- or DHA-enriched Artemia, relative EPA and DHA losses were similarly high in both treatments. In contrast, the presence of DHA in naupliar lipids increased the EPA retention, which might however be related to DHA retroconversion.