Advanced oxidation processes (AOPs) have been highly efficient in degrading contaminants of emerging concern (CEC). This study investigated the efficiency of photolysis, peroxidation, photoperoxidation, and ozonation at different pH values to degrade doxycycline (DC) in three aqueous matrices: fountain, tap, and ultrapure water. More than 99.6% of DC degradation resulted from the UV/HO and ozonation processes. Also, to evaluate the toxicity of the original solution and throughout the degradation time, antimicrobial activity tests were conducted using Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) bacteria, and acute toxicity test using the bioluminescent marine bacterium (Vibrio fischeri). Antimicrobial activity reduced as the drug degradation increased in UV/HO and ozonation processes, wherein the first process only 6 min was required to reduce 100% of both bacteria activity. In ozonation, 27.7 mg L of ozone was responsible for reducing 100% of the antimicrobial activity. When applied the photoperoxidation process, an increase in the toxicity occurred as the high levels of degradation were achieved; it means that toxic intermediates were formed. The ozonated solutions did not present toxicity.