Population matrix models are used to conduct sensitivity analyses and to assess the population-scale impacts of perturbations. The CounterPOPd software app goes one step further, in that it uses a matrix model to compare the real and hypothetical dynamics in the presence and absence of perturbations that arise from veterinary diseases. In particular, this CounterPOPd app builds on two previous apps to utilize a combinatorial optimization algorithm in conjunction with adult time series data of bald eagles to compare asymptotic and transient population dynamics with and without lead toxicosis mortalities. The first building block to this CounterPOPd app, the “EaglePOPd” software, assesses the dynamics of the current eagle population only (i.e. that with lead toxicosis. EaglePOPd is located at https://doi.org/10.7298/q4m1-se95.2. The second building block to this CounterPOPd, the “OptiPOPd” software, is a generalized version of the algorithm that may be modified to test the use of an algorithm in backfilling a symbolic matrix model using time series data. OptiPOPd is located at https://doi.org/10.7298/a416-v747. In the CounterPOPd app, comparative demographic quantities among lead and non-lead conditions include the annual abundances, bi-annual abundances, migration and dispersal, growth rates (asymptotic, transient, cumulative, and stochastic), stable stage distribution, reproductive value, survival rates, sensitivities, elasticities, damping ratios, convergence times, and more. The software also provides interpretation for each demographic quantity from the mathematical modeling, biological, ecological, and resource management perspectives. The CounterPOPd app is programmed to compare population with and without lead toxicosis in bald eagles, but the software may be modified to assess the population scale impact of other maladies in bald eagles.