Home ranges, dispersal patterns, and habitat associations of juvenile winter flounder (Pseudopleuronectes americanus) were studied using acoustic tags and three tracking systems in the Hampton-Seabrook Estuary in New Hampshire, USA. This is the first study that we know of to use electronic tags on juvenile winter flounder, and on flatfish <= 19 cm. For the first two tracking periods, both wild and cultured age 1 fish were followed by a combination of handheld hydrophones and a VRAP system. Although both cultured and wild fish maintained similar home ranges, the cultured fish immediately emigrated approximately 1000 m out of the release area while the wild fish maintained high release site fidelity. Cultured fish acclimated to the release site using in-situ cages displayed higher site fidelity after release. Cultured flounder habitat use was very similar to wild flounder habitat use in terms of bottom water temperature, dissolved oxygen, salinity, depth, and sediment composition. For the third tracking period only wild juvenile flounder were followed to discern when and at what size fish leave the estuary. Fish (n = 10) were tracked passively by an array of six submersible receivers stationed throughout the estuary. A total of 244,985 fixes were recorded by the receivers during the lifespan of the tags. The majority of these fixes were recorded by the receivers at the release site (72%) and immediately down-estuary (25%). Eighty percent of the fish remained in the immediate release area for the first two weeks, but as time at large increased, several fish dispersed down-estuary, and two individuals left the estuary for the sea. Estuary exits occurred in the winter by the largest individuals. Final positions of the tagged fish indicated that 20% had left the estuary all together, 30% of the tagged fish were still at the release site, 20% were approximately 500 m down-estuary from the release site, and 30% were unaccounted for. Understanding these movement patterns and habitat associations of both cultured and wild juvenile winter flounder is significant for developing techniques for enhancement programs and for defining essential fish habitats within this important nursery area.