Measuring the reliance of adult spawning winter flounder (Pseudopleuronectes americanus Walbaum) on estuarine habitat is problematic and may require acoustic telemetry. Efforts in various estuaries over several years have been hampered by sporadic results in detection of telemetered fish, possibly due to burial. After confirming that captive winter flounder in ambient temperature flow-through enclosures buried often and sometimes deeply, especially during low temperatures, we analyzed the effect of burial on tag signal (76.8kHz, 5s repeat rate) during periodic visitation of a grid of listening stations, vessel-towed and autonomous underwater vehicle (AUV) searches, and continuous 3-D tracking through a synchronized multiple-hydrophone positioning array. Controlled tests of tag burial in situ resulted in complete signal loss with burial at all of the tested depths. The difference between tag detection and decoding was demonstrated to be very important. Water column depth during mobile telemetry positively affected reception of tags lying on the sediment surface. Signal strength of tags on fish at liberty as recorded by an AUV-mounted hydrophone was similar during daytime and subsequent nighttime transects, as were mean counts of decoded signals per tag. However, variance was highly skewed with some tags being heard much more often at night, an expected consequence of nighttime emergence from burial, despite windier (noisier conditions) at night. Meter-scale tracking by multi-hydrophone trilateration over periods of days to weeks determined burial by timeline disruption for individual fish. The use of Markov Models, reference tags, and environmental conditions presents an opportunity to correct for biases in tag detection rates due to burial post facto. In addition, telemetry should consider nighttime efforts during the spawning season and continuous mobile (e.g. towed transect) or more frequent listening stations in search grids and closer moored hydrophone spacing than suggested by reference tags. These approaches may be relevant to other flatfishes and other fishes that bury or use benthic shelters.