Phylogeographic and genetic studies have revealed complex variation in connectivity across the Southeast Australian Biogeographic Barrier (SEABB) for intertidal rocky‐shore invertebrates. The objective of this study was to use Connie2 to test whether differences between El Niño and La Niña years alter the probability of larvae crossing the SEABB. The SEABB occurs on the SE corner of Australia and is the convergence site of two major ocean currents (Zeehan and East Australian Currents) as well as an historical land bridge connecting Tasmania to the mainland. It includes extensive sandy shore lacking suitable substrate for rocky‐shore specialists. Study locations included coastal sites from New South Wales, Victoria, and Tasmania categorised into four regions (Barrier, Eastern, Western, and Southern). Connie2, an interactive hydrodynamic modelling tool available online, was used to evaluate connectivity via larval dispersal by comparing the effect of planktonic larval duration (PLD) from five to 120 days, season of spawning, and ENSO variability (comparing La Niña and El Niño years) on the cumulative probability of dispersal between and among populations (regions) arrayed either side of the SEABB. For all years, strong connections were detected among sites within regions, even for low to moderate (less than 20% predicted dispersal) PLDs and irrespective of season. Connectivity across SEABB (between regions) was also strongly influenced by all variables but occurred only at PLD of at least 30 days for summer spawning. Connectivity across the SEABB was strongest from west to east and south to east during La Niña events. Our findings support the importance of SEABB as a barrier to dispersal. Migration across SEABB is predicted only for summer spawners (PLD ≥30 days). Predicted dispersal is only weakly influenced by El Niño and La Niña extremes, but connectivity may be altered by projected changes to the relative strengths of the Zeehan and East Australian Currents.