Abstract We monitored Peregrine Falcon (Falco peregrinus) population in Bizkaia, Northern Spain, during two decades (1998–2017). Our population increased from 34 to 47 territorial pairs, as did other European populations until the first years of the 21st century, and then declined until 34 territorial pairs in 2017. The combination of catastrophic events (Prestige oil spill), increasing rain in winter and spring, and direct and indirect mortality factors significantly affected incubation onset, productivity and population stability, which in turn could impact on the floater population. Rain in February significantly affected incubation onset, which showed a slight positive trend during the last decade. Juvenile females laid 12 days later than adults, and each adult female started incubation in the same dates every year. However, the proportion of juvenile females did not significantly increase as might have been expected. Moreover, productivity was inversely related to incubation onset dates. Rain in April and May also affected productivity, and combined with short term extreme weather events determined a decreasing productivity during the last decade. Moreover, apart from human persecution (which caused 40.30% of the known deaths of Peregrines), we found 18 cases of breeders affected by infectious diseases, also related to weather. The combined effects of these factors, and the low availability of adequate nesting sites, negatively affected (i) territorial populations, (ii) productivity, and (iii) floater population, which in turn also determined territorial population and productivity.