Fifty-four new heat flow measurements in the central troughs of the Guaymas basin support the hypothesis that they are sites of active intrusion. In the northern trough a distinct pattern of hydrothermal cooling is revealed, with venting along the western boundary fault of the trough. In the southern trough an analogous pattern is apparently superimposed upon a conductive cooling anomaly associated with a recent central intrusion. The discharge of thermal waters occurs along the boundary faults and through other faults associated with a possible horst block located in the north central floor of the southern trough. The heat flow patterns suggest that the intrusions are episodic and do not occur simultaneously along the length (15--40 km) of a spreading segment. A review of all available heat flow measurements for the Guaymas basin suggests that most of the recharge for pervasive regional hydrothermal system is limited to the central depressions, with perhaps some contribution from pore water. The discharge of thermal waters occurs predominantly in the central depressions and possibly along the boundary transform faults and fracture zones. The regions of the basin more than a few kilometers in distance from the spreading axis, although presumably underlain by a hydrothermal system, are probably not the location of numerous vents or recharge zones.