Fertilization with animal manure and sewage sludge, and the use of sewage water for irrigation, can lead to high antimicrobial concentrations in agricultural soils. Once in soil, antimicrobials can exert direct and indirect toxic effects on plants by misbalancing plant–microbe symbiotic relationships. We performed germination tests to determine the optimum germination conditions of 24 plant species (10 crop and 14 wild species). Subsequently, we analyzed the differences in oxytetracycline and sulfamethazine phytotoxicity in 19 plant species for which optimum germination conditions could be established. The root elongation of the majority of wild species was inhibited in the presence of oxytetracycline and sulfamethazine, whereas crops were mainly affected by oxytetracycline. There were no differences in sensitivity to oxytetracycline between crop and wild plant species, whereas wild plants were significantly more susceptible to sulfamethazine than crop species. Thus, to cover both productivity and biodiversity protection goals, we recommend pharmaceuticals’ predicted no-effect concentration (PNEC) values based on crop and wild plant species phytotoxicity data.