Oceanic juvenile loggerhead sea turtles, Caretta caretta, foraging in Azorean waters, are incidentally caught in drifting longlines that target swordfish, Xiphias gladius, and blue shark, Prionace glauca. Data were recorded during a longline gear modification experiment conducted in 2000. The results show that the captures are not uniformly distributed in relation to fishing effort, with 81% of the loggerheads (N = 232) caught in one-third of the sets (N = 93). The highest turtle catch rates were around the eastern group of islands, an area characterized by the presence of mesoscale eddies induced by bathymetric features. High catch rates coincided with the presence of the thermohaline front, between August and October, and when targeting blue shark. To investigate the causes of these differences we fitted a general linear model to evaluate the influence of mean depth, minimum depth, sea surface temperature (SST), soak area, soak time, moon phase and wind force on turtle and target species catch rates. These results revealed that mean depth and SST were most important for loggerhead catch rates, while minimum depth was the only significant variable for swordfish and mean depth, SST, wind force, moon phase and soak time influenced blue shark catches. The distribution of loggerhead sea turtles can be predicted by monitoring fishing areas in relation to bathymetry and SST. The impact of longline fishing could be greatly and quickly reduced by regulating the blue shark fishery and by increasing fishermen awareness for sea turtle conservation.