Toward achieving control over the kerfing through macro abrasive waterjet submerged milling, there is a need (i) to understand the influence of the water column height on the kerf quality and (ii) to develop a model for the prediction of the kerf characteristics. This study performs detailed experimentation to assess the kerf quality enhancement in submerged milling relative to the in-air milling on Al-6061 alloy. From the modeling perspective, there are very limited efforts in developing a comprehensive model that includes both the jet flow dynamics and material removal models—this is the missing link. Toward this, a comprehensive model is proposed and validated for the prediction of kerf in in-air and submerged conditions by considering (i) jet dynamics and (ii) jet–material interaction. From the experimental results, it is observed that by adopting the submerged milling, the damaged region, top kerf width and edge radius got reduced by 20.3%, 13.53%, and 22.7%, respectively. However, this enhancement in the kerf quality is associated with a reduction in the centerline erosion depth (hmax) by 12.33% and a material removal rate by 24.52%. The material removal mechanism is more uniform and directed in the submerged milling, whereas in-air is random. The proposed model predicted the kerf cross-sectional profile in submerged milling and in-air with a mean absolute error of 60 µm and 57 µm, squared Pearson correlation coefficient of 0.97 and 0.99, and the hmax with a maximum error of 1.3% and 1.4%.