This paper compares the removal degrees of selected contaminants of emerging concern in water solutions during advanced oxidation processes (AOPs), such as H2O2, O3, UV, UV/TiO2, UV/H2O2, and UV/O3. The tested micropollutants belong to the following groups: pharmaceuticals, dyes, UV filters, hormones, pesticides, and food additives. The highest removal rate of pharmaceutical compounds was observed during the UV/TiO2 process. The decomposition of hormones in this process exceeded 96% and the concentration of the UV filter dioxybenzone was reduced by 75%. The pesticide triallat and the food additive butylated hydroxytoluene were most effectively oxidized by the UV process and their removal degrees exceeded 90%. The lowest removal degree in all examined processes was observed in the case of caffeine. Toxicological analysis conducted in post-processed water samples indicated the generation of several oxidation by-products with a high toxic potential. The presence of those compounds was confirmed by the GC-MS analysis. The performance of the UV/O3 process leads to the increase of the toxicity of post-processed water solutions, especially solutions containing degradation by-products of carbamazepine, diclofenac sodium salt, acridine, trialatte, triclosan, and β-estradiol were characterized by high toxicity.