The coastal waters of Baja California Sur, Mexico, include some of the most important foraging grounds of the East Pacific green turtle Chelonia mydas. However, they are also important fishing grounds for artisanal fleets, leading potentially to high levels of bycatch mortality. We studied the impact of a small-scale gill-net fishery at San Ignacio lagoon, north-west Mexico, an important green turtle feeding ground. We conducted mortality censuses and interviewed local fishers to estimate total bycatch mortality at the lagoon. We also used marked drifters and carcasses to estimate stranding probabilities of turtles taken as bycatch. During 2006–2009 we found 262 dead turtles; 96% of the mortality occurred in May–August corresponding to the fishing season for halibut Paralichthys californicus and guitar-fish (Rhinobatus sp.). Stranding probability estimated from drifters was 0.062 (95% confidence interval, CI, 0.035–0.094), yielding a minimum mortality of 3,516 turtles during 2006–2008 (95% CI 2,364–6,057) or 1,172 animals per year. This is probably an underestimate of real mortality as the drifters have higher stranding probabilities than carcasses and most of the nets were set in the lower lagoon where carcasses rarely strand. Interviews with local fishers yielded a similar estimate of 1,087 (95% CI 901–1,286) dead turtles per year. This study is emblematic of the impact of artisanal fleets on marine turtles caused by overlap of fishing and turtle feeding areas. In 2009 strandings declined by > 97%, resulting from a change in fishing practices because of increased vigilance by enforcement authorities, underscoring the importance of law enforcement to protect threatened species.