The southern San Andreas fault has not experienced a large earthquake for approximately 300 years, yet the previous five earthquakes occurred at ~180-year intervals. Large strike-slip faults are often segmented by lateral stepover zones. Movement on smaller faults within a stepover zone could perturb the main fault segments and potentially trigger a large earthquake. The southern San Andreas fault terminates in an extensional stepover zone beneath the Salton Sea—a lake that has experienced periodic flooding and desiccation since the late Holocene. Here we reconstruct the magnitude and timing of fault activity beneath the Salton Sea over several earthquake cycles. We observe coincident timing between flooding events, stepover fault displacement and ruptures on the San Andreas fault. Using Coulomb stress models, we show that the combined effect of lake loading, stepover fault movement and increased pore pressure could increase stress on the southern San Andreas fault to levels sufficient to induce failure. We conclude that rupture of the stepover faults, caused by periodic flooding of the palaeo-Salton Sea and by tectonic forcing, had the potential to trigger earthquake rupture on the southern San Andreas fault. Extensional stepover zones are highly susceptible to rapid stress loading and thus the Salton Sea may be a nucleation point for large ruptures on the southern San Andreas fault.