Pharmaceuticals, including non-steroidal anti-inflammatory drugs (NSAIDs) like ibuprofen (IBU) and naproxen (NPX), are widely used for medical purposes but have also become prevalent environmental contaminants. However, there is limited understanding of their effects on aquatic organisms, especially regarding multigenerational and mixture exposures. This study aimed to evaluate the toxicological impacts of ibuprofen and naproxen, individually and in combination, on three generations of Daphnia carinata, a freshwater organism. Daphnids were exposed to environmentally relevant concentrations of ibuprofen and naproxen (0.1, 0.5, 2.5 µg/L and 0.1 + 0.1, 0.1 + 0.5, 2.5 + 2.5 µg/L) throughout multiple generations. The endpoints assessed were reproduction, body size, reproduction recovery, and behaviour. The results revealed that ibuprofen and naproxen negatively impacted reproduction, reducing reproduction output across generations. Additionally, daphnids exhibited changes in body size, with significant alterations observed in the F2 and F3 generations. Male individuals and ephippium were also present at all concentrations throughout all generations. Although reproduction recovery could not be observed in daphnids after one generation in clean water, the average number of neonates was higher in a few treatments in generation F4 compared to generation F3. In addition, binary mixtures of the drugs showed synergistic effects on daphnids' reproduction for most generations. The multigenerational approach provided valuable insights into the long-term effects of these NSAIDs on reproduction success and population dynamics. This study contributes to understanding the ecotoxicity of ibuprofen and naproxen in aquatic organisms, particularly in a multigenerational context and in the presence of mixture exposures.