The Selection along Estuarine Gradients in Oysters (SEGO) project is a collaborative NSF-funded effort to measure and understand the dynamics of short term adaptive change at small spatial scales. We focused on eastern oysters as an example of a common marine life history – high fecundity, complex life cycle with early larval dispersal, and sedentary (sessile for oysters) life after larval settlement. The data assembled in this data table are collections made over three years for two types of genomic analysis: (1) annual adult samples collected along the axis of the Delaware Bay estuary to capture a gradient in potentially stressful low salinities, (2) adult samples collected from mid-bay for experimental low-salinity challenge experiments, and (3) spat and broodstock collected for low salinity challenge experiments directly on wild spat or on larval progeny of broodstock collected from low vs. moderate salinity, respectively. Transect adults were collected by dredge in 2018, 2019 and 2021 from the same 5 subset of sites, each year, that the Rutgers Haskin lab consistently monitors every year to manage the oyster fishery. By piggy backing on the Haskin monitoring effort, the SEGO project has benefited from the long term data and deep understanding that Rutgers scientists have built about the Delaware Bay oyster population. 2021 was an exception because adults from an additional three sites were collected and analyzed. Two replicate challenge experiments on adults were accomplished in 2019 and 2020 using similar-size oysters collected from the highest oyster density part of the Delaware Bay population where environmental variation seems to generate the least mortality. Full details on the wild transect samples (genotype-environment association tests) and from the challenge experiment results comparing survivors vs. nonsurvivors are being prepared for publication. Spat collected in 2020 from across the salinity gradient were used for low salinity challenge experiments – results are published in Manuel et al. 2023. Broodstock collected in low vs. moderate salinity regions of the estuary in April 2021 were spawned to conduct a low salinity challenge experiment on their larvae, but larval performance and survival was too low for meaningful results.