Pharmaceuticals have become an emerging environmental protection problem due to their presence in water and soil ecosystems. Reliable cell viability biomarkers (mitochondrial and cytosol distribution of cytochrome c oxidase activity), germination, and growth of seedlings were assessed to be sensitive endpoints of diclofenac toxicity. Moreover, the content of soluble carbohydrates in seedlings of three leguminous plants was an additional indicator of germination. The tested diclofenac concentrations (from 0 to 12 mM) in the three plant species (lupin, pea, and lentil) resulted in increased activity of the enzyme in cytosol, and a decreased activity in mitochondrions. The increase of the cytochrome c oxydase activity in cytosol was most rapid in pea and slowest in lupin. The decrease in mitochondrions was gradual, yet in roots growing in the soil contaminated with 12 mM of diclofenac, from 35 to 68% of total enzyme activity leaked from the mitochondrion to the cytoplasm. The dynamics of seedling growth was a better parameter of soil contamination with diclofenac than germination. On the basis of the described morphological and biochemical features, it was found that diclofenac is decidedly less phytotoxic toward leguminous plants (lupin, pea, lentil) than e.g. sulfamethazine. The research has shown that carbohydrate metabolism is a good parameter of seedling growth, but it is not an indicator of contamination and thus cannot be applied to assess soil ecosystem contamination with medicines.