The 2015–2016 El Niño provided insight into how low-inflow estuaries might respond to future climate regimes, including high sea levels and more intense waves. High waves and water levels coupled with low rainfall along the Southern California coastline provided the opportunity to examine how extreme ocean forcing impacts estuaries independently from fluvial events. From November 2015 to April 2016, water levels were measured in 13 Southern California estuaries, including both intermittently closed and perennially open estuaries with varying watershed size, urban development, and management practices. Elevated ocean water levels caused raised water levels and prolonged inundation in all of the estuaries studied. Water levels inside perennially open estuaries mirrored ocean water levels, while those inside intermittently closed estuaries (ICEs) exhibited enhanced higher-high water levels during large waves, and tides were truncated at low tides due to a wave-built sand sill at the mouth, resulting in elevated detided water levels. ICEs closed when sufficient wave-driven sand accretion formed a barrier berm across the mouth separating the estuary from the ocean, the height of which can be estimated using estuarine lower-low water levels. During the 2015–2016 El Niño, a greater number of Southern California ICEs closed than during a typical year and ICEs that close annually experienced longer than normal closures. Overall, sill accretion and wave exposure were important contributing factors to individual estuarine response to ocean conditions. Understanding how estuaries respond to increased sea levels and waves and the factors that influence closures will help managers develop appropriate adaptation strategies.