We assessed the effects of large‐scale oceanic disturbances on the settlement rate of an abundant intertidal barnacle. Daily or weekly settlement, nearshore temperature, currents, and abundance of early‐stage barnacle nauplii and Chthamalus fissus cyprids were measured in La Jolla, California, from the inception of the large‐scale warm‐water anomaly known as the “Blob” in 2014, to 1 yr following the 2015/2016 El Niño. We also measured over 2 yr of weekly settlement rates during the 1997/1998 El Niño in La Jolla and in two Mexican sites. Settlement was low during the Blob and the 2015/2016 El Niño, but increased dramatically after its end, and rates remained high through spring 2017. Barnacle nauplii and C. fissus cyprid abundances were also low during the Blob and El Niño. Nearshore water column thermal stratification and variability of the high‐frequency cross‐shore currents, a measure of internal wave activity, declined during the Blob and El Niño, but increased at the end of El Niño. Similarly, settlement rates in the Mexican sites were low during the 1997/1998 El Niño. The reduction in settlement during the Blob and El Niño may be related to two factors: a decrease in water column stratification, which can influence internal bore larval transport and the cross‐shore distribution of larvae, and also to reduced early‐stage larval abundance, potentially related to lower reproductive output or high nauplii mortality during the disturbances.