Juvenile Chinese mitten crabs (Eriocheir sinensis) are known to use both brackish and freshwater habitats as rearing areas. The objectives of this study were to examine the habitat use and potential effects of mitten crabs in the freshwater habitats of the San Joaquin River drainage up-stream of the Sacramento-San Joaquin Delta. After several unsuccessful attempts to catch or observe mitten crabs by trapping, electrofishing, and visual observations, the study was redirected to determine the presence of crabs in the San Joaquin River (in the vicinity of Mossdale) and Suisun Marsh. Monthly surveys using baited traps in the San Joaquin River were done from June through November 2000 and in the Suisun Marsh from August through October 2000. No mitten crabs were caught in the San Joaquin River Basin and only one mitten crab was caught in Suisun Marsh. Surveys were conducted at 92 locations in the San Joaquin River Basin by deploying 352 traps for 10,752 hours of trapping effort; in Suisun Marsh, 34 locations were investigated by deploying 150 traps for 3,600 hours of trapping effort. The baited traps captured a variety of organisms, including catfishes (Ictularidae), yellowfin gobies (Acantho-gobius flavimanus), and crayfish (Decapoda). It is unclear whether the failure to capture mitten crabs in the San Joaquin River Basin and Suisun Marsh was due to ineffective trapping methods, or repre-sents a general downward trend in populations of juvenile mitten crabs in these potential rearing areas or a temporary decline related to year-class strength. Available data (since 1998) on the number of mitten crabs entrained at federal and state fish salvage facilities indicate a downward trend in the number of crabs, which may indicate a declining trend in use of the San Joaquin River Basin by juvenile mitten crabs. Continued monitoring for juvenile Chinese mitten crabs in brackish and freshwater portions of the Sacramento-San Joaquin River Basins is needed to better assess the potential population variability of this relatively new invasive species and the possible management strategies.