Power spectral analysis of heart rate variability (HRV) is a well known clinical and physiological analysis method, However, the role of the cardiovascular control systems during underwater swimming and SCUBA diving Is not completely understood. This paper examines the HRV during SCUBA diving using a recently developed microcontroller based real-time underwater acoustic biotelemetry system. The telemetered results applied to autoregressive modelling for spectral estimation suggest that the methodology can detect changes within the neurorequlatory control systems in response to the different diving regimes, This new system provides wide functional versatility for users interested in real-time underwater heart rate variability and physiological monitoring studies.