Bulgaria's brown bear (Ursus arctos L.) is a strictly protected species according to the Bulgarian Biodiversity Low. Therefore, monitoring the populations of these protected species is necessary for the effective management and conservation of their habitats. In this work, we present the features incorporated in the High-Performance Data Analysis (HPDA) service for automatic estimating of the brown bear (Ursus arctos L.) population in Bulgaria. The program software is written in C++ and includes statistical algorithms based on the maximum likelihood method. We use observed signs of bears in their habitats, collected by the route (transect) method, as input data. These signs primarily include footprints (width of fore paw footprints and length of hind paw footprints), as well as excrements and tree marks. The field data are gathered annually as part of National Field Monitoring organized by the Executive Environment Agency. Approaches for investigating the bear population by sex and age are also incorporated into this service. The output results of the HPDA service include: (i) estimates for brown bear population and density in their habitats—Alpine and Continental areas, as well as different mountains; and (ii) estimates for age structures and how threats influence the population.