The dynamics of marine invertebrate larval exchange between bay and coastal populations have received limited attention because of difficulties in determining source populations and tracking larval fate in situ. Crab larval behavior, physical transport processes, and an elemental fingerprinting technique were used to examine the exchange of larvae between San Diego Bay (SDB) and nearshore coastal habitats. Specific questions addressed for grapsid and panopeid crab larvae include: (1) Are SDB-spawned larvae exported or retained through development? (2) Do coastal-spawned larvae enter SDB? (3) Do SDB larvae exhibit tidally timed vertical migratory behavior that enhances their export or retention? (4) Do temporal changes in the horizontal distribution of crab larvae influence net transport between regions of SDB or between SDB and coastal waters? A larval fingerprinting technique, which combined elemental composition of individual larvae (Cu, Zn, Mn, Sr, Ca) with discriminant function analysis, was developed to determine the origin of field-sampled stage I Pachygrapsus crassipes (Grapsidae) zoeae. Results indacted that a significant proportion of stage I P. crassipes zoeae experience bi-directional exchange between SDB and nearshore coastal waters, contrary to inferred transport based on vertical migration patterns of P. crassipes zoeae relative to tidal phase. Trace elemental fingerprinting revealed that approximately 5% of P. crassipes zoeae sampled in the mid region of SDB originated from outside SDB, while 26% of zoeae sampled at the bay's entrance originated from outside SDB. This information, combined with instantaneous mortality rates estimated for P. crassipes zoeae, suggest that a portion of non-SDB larvae occurring within the bay are likely to complete larval development and supply recruits to adult populations. Hydrodynamic modeling simulations and field studies revealed that tidally timed vertical migratory behavior exhibited by stage I P. crassipes zoeae facilitated net transport from SDB. Lophopanopeus spp. (Panopeidae) exhibited no migratory behavior and appears to complete larval development within SDB. Heterogeneous horizontal distributions of stage I P. crassipes and Lophopanopeus spp. larvae reflect hatching sites and physical circulation features which tend to concentrate larvae. Larval flux estimates for P. crassipes indicated a net transport from inner to outer regions of SDB and ultimately into coastal waters. This export may be beneficial. Laboratory experiments suggest that P. crassipes zoeae brooded and/or cultured in nearshore coastal waters experience higher survivorship during zoeal development and yield a larger percentage of viable post-larval recruits (megalopae) than larvae reared in SDB water.