We assessed the population scale impacts of lead (Pb) toxicosis and lead exposure in Bald Eagles (Haliaeetus leucocephalus) in New York State, USA from 1990-2018. The NYCounterPOPd software uses a population matrix model to compare the real and hypothetical dynamics in the presence and absence of Pb deaths. The work specific to NY was built by adapting the CounterPOPd software (https://doi.org/10.7298/0v1k-wq39), which utilized a combinatorial optimization algorithm in conjunction with adult time series data of bald eagles in the greater Northeast US. The first building block to CounterPOPd app, the “EaglePOPd” software, assessed the dynamics of the NE eagle population only (https://doi.org/10.7298/q4m1-se95), while the second building block to CounterPOPd, the “OptiPOPd” software, was a generalized version the algorithm that is used to backfill a symbolic matrix model using time series data (https://doi.org/10.7298/a416-v747). The NYCounterPOPd segment of this package tailored the CounterPOPd software to the region of New York.