Disruption of food availability by unfavorable physical processes at energetically demanding times can limit recruitment of migratory species as predicted by the match–mismatch hypothesis. Identification and protection of disruption-resistant habitat could contribute to system resilience. For example, horseshoe crab Limulus polyphemus spawning and shorebird stopover must match temporally in Delaware Bay for eggs to be available to shorebirds. Onshore winds that generate waves can create a mismatch by delaying horseshoe crab spawning. We examined effects of beach characteristics and onshore winds on spawning activity at five beaches when water temperatures were otherwise consistent with early spawning activity. Onshore winds resulted in reduced spawning activity during the shorebird stopover, when spawning typically peaks in late May. During the period with high onshore wind, egg density was highest on the foreshore exposed to the lowest wave heights. Onshore wind was low in early June, and spawning and egg densities were high at all sites, but shorebirds had departed. Beaches that can serve as a refuge from wind and waves can be identified by physical characteristics and orientation to prevailing winds and should receive special conservation status, especially in light of predicted increases in climate change-induced storm frequency. These results point to a potential conservation strategy that includes coastal management for adapting to climate change-induced mismatch of migrations.