Vertical and cross-shore distributions and abundances of shallow-water barnacle larvae were characterized in La Jolla, southern California (USA), during a 2 yr period. Five stations located within 1 km of shore and ranging from 4-12 m water depths were sampled intensively in 2 m depth intervals during 27 cruises throughout spring-summer (April-July) and fall-winter (October-December) of 2014 and 2015. Larval abundances significantly decreased from 2014 to 2015, which could be related to the arrival of a warm-water anomaly (the so-called ‘Blob’) in 2014 and El Niño conditions in 2015. Despite the presence of these large-scale regional disturbances, vertical and cross-shore larval distributions were consistent throughout the 2 yr study period. Early-stage nauplii and Chthamalus fissus cyprids tracked bottom depth, and cyprids were on average deeper than nauplii. Vertical distributions were not related to the mid-depth of the thermocline or thermal stratification. Early-stage nauplii had a broader cross-shore distribution than cyprids, which were concentrated at inshore stations. Nearshore cyprid concentration had a positive relationship with thermal stratification, and the center of distribution of cyprids was farther offshore during fall-winter when stratification decreased. These results suggest that thermal stratification elicits enhanced behavioral control of cyprids to remain close to shore and reach the adult habitat.