We use geophysical and geochemical data and an impersonalized catalogue of ambulance calls for the period 2015–2017 to study the morbidity of the population in Petrozavodsk, which is located in a sub-Arctic region with challenging climatic, weather and geomagnetic conditions. Temporal, spatial and other emergency call distributions, reflecting the effects of a variety of factors on morbidity, have been investigated. The effect of geomagnetic activity on the number of ambulance calls with myocardial infarction and stenocardia diagnoses and a reduction in the number of calls on weekends and holidays were corroborated. Soil pollution patterns in the city did not correlate with the distribution of the number of ambulance calls associated with common diseases in residential areas. The results reflect the structure of the morbidity of the urban population, and do not contradict the known environmental models.