This study aimed to investigate the effect of cold and thermoneutral water immersion on post-exercise parasympathetic reactivation, inferred from heart rate (HR) recovery (HRR) and HR variability (HRV) indices. Twelve men performed, on three separate occasions, an intermittent exercise bout (all-out 30-s Wingate test, 5 min seated recovery, followed by 5 min of submaximal running exercise), randomly followed by 5 min of passive (seated) recovery under either cold (CWI), thermoneutral water immersion (TWI) or control (CON) conditions. HRR indices (e.g., heart beats recovered in the first minute after exercise cessation, HRR 60 s) and vagal-related HRV indices (i.e., natural logarithm of the square root of the mean of the sum of the squares of differences between adjacent normal R–R intervals (Ln rMSSD)) were calculated for the three recovery conditions. HRR 60 s was faster in water immersion compared with CON conditions [30 ± 9 beats min − 1 for CON vs. 43 ± 10 beats min − 1 for TWI ( P = 0.003) and 40 ± 13 beats min − 1 for CWI ( P = 0.017)], while no difference was found between CWI and TWI ( P = 0.763). Ln rMSSD was higher in CWI (2.32 ± 0.67 ms) compared with CON (1.98 ± 0.74 ms, P = 0.05) and TWI (2.01 ± 0.61 ms, P = 0.08; aES = 1.07) conditions, with no difference between CON and TWI ( P = 0.964). Water immersion is a simple and efficient means of immediately triggering post-exercise parasympathetic activity, with colder immersion temperatures likely to be more effective at increasing parasympathetic activity.