Overfishing, bycatch, and habitat loss and alteration during the late 19th century to the end of the 20th century caused significant declines in Atlantic Sturgeon Acipenser oxyrinchus stock abundances along the Atlantic coast. To prevent further stock reductions, a coastwide harvest moratorium was implemented in 1998. With fishery‐dependent data unavailable to inform stock management, fishery‐independent surveys contribute vital information for monitoring population trends by providing data for evaluating the effectiveness of the moratorium and for informing recovery planning. In 2004, a standardized monitoring survey was developed to assess trends in the relative abundance of juvenile Atlantic Sturgeon in the Hudson River, New York. The multimesh anchored gill‐net survey randomly sampled locations in soft, deep depositional areas of Haverstraw Bay from late February through early May. Predicted length‐at‐age relationships were used to infer annual age structure and to examine the relationships between age and annual catch rates. Generalized additive regression modeling was used to describe the relationships between the environmental variables and catch rates and to standardize the abundance index to account for variability in environmental conditions over time. Atlantic Sturgeon catch rates generally increased with increasing water temperature and salinity, and the standardized abundance index (accounting for environmental variability) was highly correlated with the nominal abundance index. In the 16 years of annual monitoring, there has been a significant increase in the relative abundance of juvenile Atlantic Sturgeon. The average catch rate in recent years (2012–2019) is more than twice that observed during the first 8 years (2004–2011) of the survey, as the effects of the moratorium are expected to be delayed due to the long maturation period of Atlantic Sturgeon. These trends suggest that juvenile Atlantic Sturgeon in the Hudson River may be recovering in response to the moratorium and demonstrate the need for long‐term fisheries‐independent monitoring to document abundance trends in slow‐maturing, long‐lived species.