Environmental DNA (eDNA) tools can address gaps in fish assessment data while reducing the cost and the impact of sampling on threatened anadromous alosine fishes in Chesapeake Bay. Here, I tested the ability of high-frequency eDNA sampling of river herring to predict fish abundances from sonar-based fish counts on the Choptank River and developed and validated novel species-specific eDNA assays for American and hickory shads. River herring eDNA concentrations from daily eDNA sampling were highly correlated to sonar-based fish counts (Spearman’s Rho = 0.84). This relationship informed a model that could accurately predict fish count from eDNA and relevant covariates (R2 = 0.88). The two new shad assays are highly specific and quantitative, and field testing validated detections in Delaware, Maryland, and North Carolina. This work provides a set of eDNA monitoring tools for the Mid-Atlantic alosines and highlights the capacity for eDNA data to generate quantitative metrics of fish abundance.