Ozonation of natural waters is typically associated with the formation of carbonyl compounds (aldehydes, ketones and ketoacids), a main class of organic disinfection byproducts (DBPs). However, the detection of carbonyl compounds in water and wastewater is challenged by multiple difficulties inherent to their physicochemical properties. A non-target screening method involving the derivatisation of carbonyl compounds with p-toluenesulfonylhydrazine (TSH) followed by their analysis using liquid chromatography coupled to electrospray ionisation high-resolution mass spectrometry (LC-ESI-HRMS) and an advanced non-target screening and data processing workflow was developed. The workflow was applied to investigate the formation of carbonyl compounds during ozonation of different water types including lake water, aqueous solutions containing Suwannee River Fulvic acid (SRFA), and wastewater. A higher sensitivity for most target carbonyl compounds was achieved compared to previous derivatisation methods. Moreover, the method allowed the identification of known and unknown carbonyl compounds. 8 out of 17 target carbonyl compounds were consistently detected above limits of quantification (LOQs) in most ozonated samples. Generally, the concentrations of the 8 detected target compounds decreased in the order: formaldehyde > acetaldehyde > glyoxylic acid > pyruvic acid > glutaraldehyde > 2,3-butanedione > glyoxal > 1-acetyl-1-cyclohexene. The DOC concentration-normalised formation of carbonyl compounds during ozonation was higher in wastewater and SRFA-containing water than in lake water. The specific ozone doses and the type of the dissolved organic matter (DOM) played a predominant role for the extent of formation of carbonyl compounds. Five formation trends were distinguished for different carbonyl compounds. Some compounds were produced continuously upon ozonation even at high ozone doses, while others reached a maximum concentration at a certain ozone dose above which they decreased. Concentrations of target and peak areas of non-target carbonyl compounds during full-scale ozonation at a wastewater treatment plant showed an increase as a function of the specific ozone dose (sum of 8 target compounds ∼ 280 µg/L at 1 mgO3/mgC), followed by a significant decrease after biological sand filtration (> 64–94% abatement for the different compounds). This highlights the biodegradability of target and non-target carbonyl compounds and the importance of biological post-treatment.