In a well-functioning slow sand filter (SSF), dissolved oxygen (DO) is crucial for enabling aerobic processes and microbiota growth. Given that DO supply is predominantly via the feed water, flow pauses (e.g., during cleaning) may trigger anoxic/anaerobic conditions in the stagnant filter bed. Underwater skimming (UWS) is an advanced cleaning technique that employs a skimmer with a shrouded blade, mounted on a mobile platform, to remove the fouling layer composed of sand and particles in order to improve the efficiency of slow sand filtration. As UWS results in changes to the flow pattern of the SSF, a mathematical model was developed to predict DO utilization after a flow perturbation associated with UWS operation. The model was based on a depth resolved measurement of specific oxygen utilization derived from a full scale SSF. Pilot plant experiments monitored DO in the feed and filtrate of SSFs cleaned using underwater and conventional dry skimming techniques. The highest oxygen utilization was in the Schmutzdecke layer, with additional demand imposed by the presence of a granular activated carbon (GAC) sandwich layer. It was observed that pseudo-steady state conditions occurred following filter ripening, where DO utilization, driven by biological activity, remained relatively constant regardless of filter cleaning technique. For flow pauses between three and 24 h, the pause duration's importance decreased, while the hydraulic loading rate became the critical factor for DO recovery in the filter. Additionally, introducing a ‘sweetening flow’ during UWS ensured a continuous DO supply, facilitating quicker DO replenishment post-cleaning. The model reliably predicted filtrate DO within ±0.6 mg/L, demonstrating its operational utility, especially in the optimisation of UWS methodology. As such, UWS can be applied to clean SSFs with the methodology modified to prevent any detrimental effects to DO management within the filter. This study predicted DO dynamics in SSFs, advancing UWS techniques and could be applied for enhancing water treatment strategies by filtration.