The vaquita (Phocoena sinus) is a critically endangered small cetacean found only in the upper Gulf of California, where fisheries bycatch remains an acute threat. Cost, shallow heavily fished areas, and the vaquitas extreme avoidance of noisy motorized vessels argue against using large vessels typically used for visual line transect surveys. Towed hydrophone surveys, using RainbowClick semi-automatic detection software, were carried out from a 24' sailing trimaran in autumn 2008. Ultrasonic (∼130 kHz) vaquita echolocation clicks were reliably detected and tracked using classification parameters developed for harbor porpoise. Transects were sailed on 49% of days and 31 groups were detected within the vaquitas known range and in areas not easily surveyed using traditional methods. Although very high levels of ambient noise presented challenges for acoustic monitoring, perpendicular distances were calculated to 30 groups giving an estimated strip half-width of 198 m. The detection algorithm has since been implemented in PAMGUARD software and significantly improved using survey data. Shallow, heavily fished areas remain difficult for estimating and monitoring trends in abundance. Towed arrays proved effective for the former and may remain the only alternative for the latter. Precision is likely to remain low for the quick detection of small rates of increase.