The panmictic population of American eel (Anguilla rostrata) is at risk, making any region that supports enhanced production important from a recovery perspective. Strong glass eel runs to a small number of rivers along the Atlantic coast of Nova Scotia are thought to indicate high productivity, partially buffering declines occurring in other regions. However, contrary to glass eel indices of recruitment, an index representing older juveniles has strongly declined in riverine habitats throughout Nova Scotia from 1995 to 2005, with evidence of substantial differences in relative abundance among watersheds. This suggests that glass eel indices may not reflect trends of older juveniles and consequently that the contribution of Atlantic coast rivers to population persistence may be overstated. More recent monitoring from two rivers shows divergent trends in juvenile eel abundance, underscoring the importance of widespread surveys to assess changes in regional productivity. Further evaluation of the watershed characteristics associated with higher juvenile abundance would aid in understanding differences in productivity among watersheds and possibly in facilitating increased spawning escapement for American eel.