Cyanobacterial blooms often produce different classes and chemical variants of toxins such as dietary protease inhibitors (PIs) that affect the keystone grazer Daphnia. However, it has been shown that Daphnia populations are able to locally adapt to frequently occurring dietary PIs by modulating their digestive proteases. Up until now, local adaptation has exclusively been tested by making use of single cyanobacterial strains and by measuring average population tolerance. In contrast, we measured juvenile somatic growth rates and egg numbers of several individual clones per each of three different D. magna populations that have previously been found to be either tolerant or sensitive to the Microcystis strain BM25. Clones from the three D. magna populations were either treated with BM25 that produces three different protease inhibitor variants of the class of Ahp-cyclodepsipeptides or another Microcystis strain that produces two other Ahp-cyclodepsipeptide variants. Subsequently, the population growth was calculated as mean of the single-clone growth rates. Both tolerant populations (which originate from ponds with a cyanobacterial history) proved to be similarly tolerant to both Microcystis strains. However, single genotypes of the populations differed in their response to the different strains. Both the tolerant and the sensitive populations contained both sensitive and tolerant genotypes but in different proportions. Furthermore, the genotypes from the sensitive population showed a higher variance in response to one or both strains. Trade-offs between somatic growth rate and clutch size were found in one of the tolerant populations that originated from a pond where cyanobacteria were frequent in the past but completely absent since the pond's restoration. Because of those intra-population difference, we conclude that the tolerant populations were putatively selected by different Ahp-cyclodepsipeptide variants in the past and that all populations still possess the potential to adapt to other environmental conditions by genotype frequency shifts.