In this paper we present a study on areas of habitation in St. Petersburg, Russia, which are actively used and perceived by city dwellers as coherent units. The motivation behind the study is to define generic urban areas formed by actual user experience and different from administrative division to improve urban management of the city territory. We employ mixed methods approach to account both for users’ practices in urban space, based on analysis of check-in data, and users’ perception of urban space, based on analysis of mental maps. The clustering algorithm is based on spatial and social proximity indexes and has been validated through the results of the mental mapping survey. The dataset of check-ins is retrieved from VKontakte social network, the most popular one for St. Petersburg and for Russia, and comprises 6128 venues with 763079 check-ins collected for December 2017–February 2018 time period. The mental mapping has been conducted within 39 users of different age and gender, representing different areas of the city under study. We compare the borders of the areas of habitation with the map of administrative division, consider functional load of the areas in different areas of the city, define environmental factors which form the borders, give suggestions on how knowledge on areas of habitation could inform and improve urban management practice.