Omega-3 (ω3) and -6 (ω6) polyunsaturated fatty acids (PUFA) are essential for all aquatic animals, but their dietary availability can be highly heterogeneous in space and time. The way consumers retain PUFA across such heterogeneous feeding conditions remains poorly understood. In a series of feeding experiments, we investigated how retention efficiencies (i.e. amount in consumer biomass/amount ingested) of PUFA and bulk carbon responded to heterogeneous PUFA intake in Daphnia magna. Heterogeneous PUFA intake was achieved by exposing D. magna to algal diets of different PUFA content and composition for specific time periods. The retention efficiency of carbon did not change among dietary treatments. At shorter exposure to PUFA-rich diet, retention efficiencies of most PUFA were 2–3 times higher than that of bulk carbon, clearly indicating PUFA bioaccumulation in D. magna. Increasing exposure to PUFA-rich diet caused exponential decrease of retention efficiencies for most PUFA. However, D. magna receiving more PUFA were richer in these compounds despite lower retention efficiency. Eicosapentaenoic (20:5ω3) and arachidonic acid (20:4ω6) and their precursors were always supplied in the same proportions (3.6:1), but the 20:5ω3/20:4ω6 ratio in D. magna (an important measure of nutritional quality for consumers) increased with exposure time to these PUFA from 2.2:1 to 3.8:1, thus eventually matching the diet. Our results suggest that D. magna is an efficient gatherer, accumulator, and repository of PUFA under low/fragmented dietary availability. However, at higher availabilities, PUFA are not always bioaccumulated in D. magna. Hence, the efficiency of PUFA transfer by daphnids in food webs may depend on temporal PUFA availability and its range of variation. Finally, we show that heterogeneity in PUFA intake may also affect higher trophic levels by influencing nutritionally critical PUFA ratios of zooplankton.