1. Horseshoe crab population sizes and trends have been previously studied using surveys of spawning adults and counts of eggs from surface (top 5 cm) and deep (20 cm) sediment samples. The correlations between surface and deep eggs were studied at two locations, Delaware Bay and Jamaica Bay, USA, and the correlations between egg densities and spawning counts were examined in Jamaica Bay.2. There were significantly higher densities of eggs in deep sediments than in surface sediments. Only about 10% of the variability in surface egg density was explained by deep egg density. The numerical patterns between surface and deep eggs were similar between Delaware Bay and Jamaica Bay and across sampling dates.3. Nearly 20% of the deep samples in the combined data from Delaware Bay and Jamaica Bay with an egg density of ≥100,000 m −2 had zero surface eggs.Therefore, the use of surface eggs as an indicator of habitat suitability and spawning intensity may seriously underestimate the importance of a beach for spawning horseshoe crabs. 4. When paired with nearest survey date, Jamaica Bay spawning indices did not predict deep or surface egg densities. This may be related to a temporal mismatch between survey methods, the extreme overdispersion (patchiness) of the eggs, and/or the dynamics of egg distribution after exhumation. 5. Both egg density and spawning surveys can provide useful data on habitat suitability for horseshoe crabs and can offer excellent opportunities for student and citizen scientist engagement. More labour is required for egg surveys than spawning surveys because of the time required to sample, sort, and enumerate the eggs.