Toxin-producing cyanobacteria can be harmful to aquatic biota, although some grazers utilize them with often beneficial effects on their growth and reproduction. It is commonly assumed that gut microbiota facilitates host adaptation to the diet; however, the evidence for adaptation mechanisms is scarce. Here, we investigated the abundance of genes in the gut of the Baltic copepods and during cyanobacteria bloom season (August) and outside it (February). The genes are unique to microcystin and nodularin degraders, thus indicating the capacity to break down these toxins by the microbiota. The genes were expressed in the copepod gut year-round, being >10-fold higher in the summer than in the winter populations. Moreover, they were significantly more abundant in than . To understand the ecological implications of this variability, we conducted feeding experiments using summer- and winter-collected copepods to examine if/how the abundance in the microbiota affect: (1) uptake of toxic , (2) uptake of a non-toxic algal food offered in mixtures with , and (3) concomitant growth potential in the copepods. The findings provide empirical evidence that the occurrence of genes in the copepod microbiome facilitates nutrient uptake and growth when feeding on phytoplankton mixtures containing nodularin-producing cyanobacteria; thus, providing an adaptation mechanism to the cyanobacteria blooms.