The Saco River estuary is a narrow estuary in southern Maine, for which the fauna has not been described in nearly 30 years. Beach seining, otter trawling, and beam trawling were conducted between April and October of 2007 and 2008 to assess seasonal variation in fish assemblage structure. Twenty-four species were observed over the two sampling seasons, and nearly all species were at lengths indicative of juvenile age. Clupea harengus (Atlantic Herring), Pseudopleuronectes americanus (Winter Flounder), Anguilla rostrata (American Eel), Microgadus tomcod (Atlantic Tomcod), Pomatomus saltatrix (Bluefish), and Osmerus mordax (Rainbow Smelt) are either commercially or recreationally valuable, while Acipenser oxyrynchus oxyrynchus (Atlantic Sturgeon), Alosa aestivalis (Blueback Herring), and Rainbow Smelt are federally listed species of concern. Substantial historical assemblage changes were observed, including both the loss of commercially important species and the addition of species of concern. Regular monitoring of estuarine habitats is necessary to identify changes in assemblages and to better understand potential drivers of ecosystem change.