Describing habitat use by stream fishes is important from both basic ecological and fisheries management points of view. The most widely used methods of measuring habitat use vary in degree of effort required, level of intrusiveness and in the level of spatial and temporal resolution. In this paper, we describe a remote monitoring technique that can provide detailed and continuous data on habitat use of individual fish in the field. The technique is based on the passive integrated transponder (PIT) system, in which a newly developed flat-bed antenna is placed on the stream bottom and simply requires a PIT-tagged fish to swim over it. We present data obtained from work using this new technology on brown trout (Salmo trutta) in stream enclosures, in which we describe habitat use and temporal patterns of movement by individuals and relate such data to growth rate and sex of the individual fish as well as to pool depth and time of day. In addition, we describe the range of applications of the flat-bed PIT-antenna as well as the advantages and disadvantages of using the system.