A substantial problem in determining whether anthropogenic noise affects marine animals is measuring how an animal responds to a noise source that is located in a remote pelagic environment and is ephemeral in nature. We are interested in measuring northern fur seal reactions to ship noise in the Bering Sea, Alaska, where the fur seals have started to decline. The timing of their decline coincides with an increased probability of interaction with the pollock fishing fleet. Whether fishing activity affects fur seal behavior, via direct competition for fish and/or indirect competition (e.g., acoustic disturbance or vessel avoidance), is unknown and difficult to study. We began by developing procedural tools to measure encounter rates and animal response. We deployed acoustic dataloggers on lactating females in order to monitor for ship signatures. This was referenced to movement data from satellite position fixes and pressure data from dive records. The combined dataset provides assays that measure an animal’s movement (i.e., direction, speed, and relative effort via stroke rate), its overall activity budget (i.e., traveling, diving, and resting), and the pattern of diving behavior. The assays are now being field tested with a new set of instrument deployments during the 2004 fur seal breeding season.