Reliable quantification of natural and anthropogenic gas release (e.g.\ CO$_2$, methane) from the seafloor into the ocean, and ultimately, the atmosphere, is a challenging task. While ship-based echo sounders allow detection of free gas in the water even from a larger distance, exact quantification requires parameters such as rise speed and bubble size distribution not obtainable by such sensors. Optical methods are complementary in the sense that they can provide high temporal and spatial resolution of single bubbles or bubble streams from close distance. In this contribution we introduce a complete instrument and evaluation method for optical bubble stream characterization. The dedicated instrument employs a high-speed deep sea stereo camera system that can record terabytes of bubble imagery when deployed at a seep site for later automated analysis. Bubble characteristics can be obtained for short sequences of few minutes, then relocating the instrument to other locations, or in autonomous mode of intervals up to several days, in order to capture variations due to current and pressure changes and across tidal cycles. Beside reporting the steps to make bubble characterization robust and autonomous, we carefully evaluate the reachable accuracy and propose a novel calibration procedure that, due to the lack of point correspondences, uses only the silhouettes of bubbles. The system has been operated successfully in up to 1000m water depth in the Pacific Ocean to assess methane fluxes. Besides sample results we also report failure cases and lessons learnt during development.