We aimed to investigate how acute and long-term effects of atrial arrhythmias affect the desaturation severity and characteristics determined from the oxygen saturation signal in OSA patients. 520 suspected OSA patients were included in retrospective analyses. Eight desaturation area and slope parameters were calculated from blood oxygen saturation signals recorded during polysomnographic recordings. Patients were grouped based on whether they had previously diagnosed atrial arrhythmia (i.e., atrial fibrillation (AFib) or atrial flutter) or not. Furthermore, patients with a previous atrial arrhythmia diagnosis were sub-grouped based on whether they had continuous AFib or sinus rhythm during the polysomnographic recordings. Empirical cumulative distribution functions and linear mixed models were utilized to investigate the connection between diagnosed atrial arrhythmia and the desaturation characteristics. Patients with previous atrial arrhythmia diagnosis had greater desaturation recovery area when the 100% oxygen saturation baseline reference was considered (β=0.150-0.127, p≤0.039) and more gradual recovery slopes (β=-0.181- -0.199, p<0.004) than patients without a previous atrial arrhythmia diagnosis. Furthermore, patients with AFib had more gradual oxygen saturation fall and recovery slopes than patients with sinus rhythm. Desaturation recovery characteristics in the oxygen saturation signal contains essential information about the cardiovascular response to hypoxemic periods. More comprehensive consideration of the desaturation recovery section could provide more detailed information about OSA severity, for example when developing new diagnostic parameters.