Passive integrated transponder (PIT) technology is rarely utilized in estuaries due to (1) saline water's attenuation of an antenna's electromagnetic field, (2) rapidly changing water properties and levels, and (3) the challenges of installing and maintaining antennas in silty, brackish conditions. We present methods for the construction and installation of antennas that can detect 12-mm full-duplex PIT tags in salinities up to 33‰. We evaluated their reading performance under variable water salinities, temperatures, and depths in the upper estuaries of three streams. We found that water depth, salinity, and temperature were all negatively correlated with antenna current, but that the relative importance of these variables varied depending upon aspects of the antenna deployment. Since our antennas held amperage levels adequate for maintenance of a complete electromagnetic field throughout all test conditions, we suggest that successful detection was more dependent upon the antenna system's coverage of the water column and the swimming path of fish through the antenna system than individual antenna performance. In addition to fish, this technology could be applied to studies of mammals, crustaceans, and particles transported through estuarine channels.