Agriculture is fundamental for human development, but it may also have a range of unwanted effects on ecosystems when pesticides inadvertently enter the environment. We determined the toxicity of difenoconazole and atrazine, as well as their photodegradation products, on the bioindicators Lemna minor and Daphnia magna. For L. minor, we assessed the number of leaves, biomass, and chlorophyll content exposed to different concentrations of difenoconazole (0–8 mg/L) and atrazine (0–3.84 mg/L). For D. magna, we assessed the mortality to difenoconazole (0–1.6 mg/L) and atrazine (0–80 mg/L). We found that the higher the concentrations of the pesticides, the higher the toxicity for both bioindicators. In L. minor, the highest toxicity for atrazine was 0.96 mg/L, whereas for difenoconazole, it was 8 mg/L. For D. magna, the 48 h LC50 for difenoconazole was 0.97 mg/L, while for atrazine, it was 86.19 mg/L. For L. minor, the toxicity of difenoconazole and atrazine was not different compared to that of their photodegradation products. In contrast, for D. magna, difenoconazole, but not atrazine, was more toxic compared to its respective photodegradation products. Pesticides are a serious threat to aquatic biota, and their photodegradation products remain toxic in the environment. Additionally, the use of bioindicators can help monitor these pollutants in aquatic ecosystems in countries where the application of pesticides is imperative for agricultural production.