Assessment of population structure is often used to detect and analyse the impact on marine fauna of environmental factors or commercial fishing. A primary tool in the characterisation of population structure is the distribution of the lengths of a large sample of individual specimens of a particular species. Rather than use relatively unreliable visual estimates by SCUBA divers, an under-water stereo video system has been developed to improve the accuracy of the measurement of lengths of highly indicative species such as reef fish. In common with any system used for accurate measurements, calibration of the camera system is of paramount importance to realise the maximum possible accuracy from the system. Further, the determination of the relative orientation of the two cameras is vital to the correct estimation of fish lengths. Also at issue is the stability of the calibrations and relative orientation of the cameras during deployments to capture video sequences of marine life, as any variations will inevitably lead to systematic errors and therefore inaccuracies in the measured lengths. This paper describes a series of experiments concerning the determination and testing of camera calibration, relative orientation and stability of the underwater stereo video system. The strategy for the integrated determination of calibration and orientation is described. Variations in calibration and orientation parameters are quantified in terms of magnitude and significance. Finally, the detected variations are analysed for the propagated effects on object space accuracy.