Overfishing and habitat loss have reduced Pseudopleuronectes americanus (Winter Flounder) populations within the Gulf of Maine (GOM), and despite strict management regulations, abundance is still low. As the GOM continues to warm, there is need to characterize Winter Flounder movements in estuaries to better understand essential habitat use. To characterize movements and habitat use of Winter Flounder, we tagged 17 juvenile flounder (115–170 mm) with acoustic transmitters (Vemco V7-2x) and monitored them using passive tracking over a 4-month period between July and November 2017 in the Saco River Estuary (SRE) in southern Maine. Movement within the SRE was highly variable, with cumulative movements of individual tracked flounder varying between 0 m (e.g., detected only at the release site) and 17,016 m. Tagged flounder were most often present in moderate (15–20 °C) temperatures and salinities (18–26 ppt), and were rarely observed in the highest temperatures (>20 °C) and salinities (>26 ppt). Movements upstream and downstream by flounder appeared to be tidally driven, with most downstream movements occurring during ebb tides and upstream movements during incoming tides. In addition, large flounder moved further away from freshwater, while small flounder either stayed within the river mouth's jetties or moved upstream. The speeds of flounder movements among receiver locations (mean = 4.49 body lengths per second, SE = 0.85) were much faster than expected for flatfish, potentially facilitated by use of tides. The GOM populations of Winter Flounder may benefit from management of juvenile habitat as environmental conditions change.