To prevent grounding of ships and collisions between ships in shallow coastal waters, an underwater data collection and communication network (ACME) using underwater sounds to encode and transmit data is currently under development. Marine mammals might be affected by ACME sounds since they may use sound of a similar frequency (around 12 kHz) for communication, orientation, and prey location. If marine mammals tend to avoid the vicinity of the acoustic transmitters, they may be kept away from ecologically important areas by ACME sounds. One marine mammal species that may be affected in the North Sea is the harbour seal (Phoca vitulina). No information is available on the effects of ACME-like sounds on harbour seals, so this study was carried out as part of an environmental impact assessment program. Nine captive harbour seals were subjected to four sound types, three of which may be used in the underwater acoustic data communication network. The effect of each sound was judged by comparing the animals' location in a pool during test periods to that during baseline periods, during which no sound was produced. Each of the four sounds could be made into a deterrent by increasing its amplitude. The seals reacted by swimming away from the sound source. The sound pressure level (SPL) at the acoustic discomfort threshold was established for each of the four sounds. The acoustic discomfort threshold is defined as the boundary between the areas that the animals generally occupied during the transmission of the sounds and the areas that they generally did not enter during transmission. The SPLs at the acoustic discomfort thresholds were similar for each of the sounds (107 dB re 1 lPa). Based on this discomfort threshold SPL, discomfort zones at sea for several source levels (130–180 dB re 1 lPa) of the sounds were calculated, using a guideline sound propagation model for shallow water. The discomfort zone is defined as the area around a sound source that harbour seals are expected to avoid. The definition of the discomfort zone is based on behavioural discomfort, and does not necessarily coincide with the physical discomfort zone. Based on these results, source levels can be selected that have an acceptable effect on harbour seals in particular areas. The discomfort zone of a communication sound depends on the sound, the source level, and the propagation characteristics of the area in which the sound system is operational. The source level of the communication system should be adapted to each area (taking into account the width of a sea arm, the local sound propagation, and the importance of an area to the affected species). The discomfort zone should not coincide with ecologically important areas (for instance resting, breeding, suckling, and feeding areas), or routes between these areas.