Eastern oyster (Crassostrea virginica) populations are sparse and fragmented throughout the Hudson River Estuary (HRE). For oyster restoration efforts to collectively build a self-sustaining population, larval connectivity between isolated breeding populations is required. This study analyzes patterns of spat settlement at two spatial scales: the entire upper estuary and more intensively in Hudson River Park (HRP), Manhattan where there is a relatively new restoration site. Oyster sampling sites were located in both fresh or brackish water (upstream near Mario Cuomo Bridge) and near-oceanic salinities (downstream near lower Manhattan). Two breeding populations exist along this gradient: remnant native oysters in the Tappan Zee/Haverstraw Bay (TZHB) area near Tarrytown, and aquaculture oysters used for restoration in HRP. Native oysters are genetically distinct from domesticated aquaculture oysters, which provided a means to distinguish spat and adult reference samples by genotyping 243 DNA variants in reference adult samples and each spat. At a large scale, spat settlement abundances were analyzed in 2022 and 2023 to map the temporal and spatial distribution of recruitment. Connectivity patterns between populations were inferred with genomic assays. Spat abundances were highest upstream in 2022 and flipped to be highest downstream near HRP in 2023. Almost all of the 2095 spat genotyped in both years were genetically more similar to TZHB native oysters, indicating they originated from parents in the upstream population. This suggests that recruitment contributions from the HRP oysters were below detection power in this study or occurred in unsampled portions of the estuary. Histological gonad analyses confirm that adult restoration oysters in HRP spawned in 2023, so finding where their offspring disperse remains an important challenge. At a small scale, spat abundance was compared among 2023 HRP sites to test whether altered river flow at certain piers (baffle effects) increases larval recruitment. Baffle affected piers did not show a significantly greater amount of spat when compared to controls, though a significantly higher number of spat/shell were found at piers at the northern end of HRP relative to the south. Further study to confirm a baffle mechanism can be leveraged to enhance settlement.