Spillover of Highly Pathogenic Avian Influenza (HPAI) to backyard poultry via migratory birds threatens the poultry industry and public health. To improve the understanding of spillover events, we developed a stochastic compartmental mathematical model of HPAI transmission dynamics at the waterfowl-backyard poultry interface in a high-risk area for HPAI introduction into poultry. The model described the infection spread among resident and migratory waterfowl and backyard poultry farms and was validated with historical outbreak data in backyard poultry farms and swan mortalities. We used the model to assess the impact of the timing and duration of migratory birds´ stopover period on the probability of HPAI infection in backyard poultry farms. Additionally, we predicted mortality in a sentinel bird species and assessed the impact of HPAI virulence and immunity in a resident reservoir species on the HPAI transmission dynamics. The stopover duration of the reservoir species predicts the HPAI infection probability in backyard poultry farms from waterfowl communities, but the stopover timing has no effect. HPAI virus virulence and immunity against the virus impact the transmission risk to backyard poultry. Understanding factors influencing reservoir species´ migration stopover duration in a location will aid HPAI outbreak forecasting and control in backyard poultry farms.