In 2016, net migration was positive for the second year in a row, with immigration exceeding emigration as 14,822 persons took up residence in Estonia and 13,792 persons left Estonia during the year. As external migration is often left unregistered by Estonian residents, as of 2015, Statistics Estonia also takes into account unregistered migration in addition to registered migration and as a result, the migration flows since 2015 have been larger compared to previous years.

14,053 persons were born and 15,392 persons died in 2016. The number of births increased compared to the previous three years. The number of women of childbearing age (15-44) has decreased in ten years by more than 36,000 women, but the number of women in active childbearing age (25-34) has remained relatively stable and is beginning to decrease only now that the small generations of the 1990s are reaching that age. The fact that the number of births remains at the 2012 level means that the number of children born per woman has increased. The number of deaths has been stable in the past seven years, remaining between 15,000-16,000.

When looking at demographic processes by sex, it appears that in one year, the number of men in the population increased by 830 and the number of women decreased by 1,139. In 2016, almost 700 more boys were born than girls and as the share of women in the older age groups is bigger, there are more deaths among women than among men. Net migration was positive for both sexes, meaning that immigration exceeded emigration, however the number of men grew by almost 600 more persons than the number of women due to net migration.

By county, population numbers increased in Harju and Tartu Countie but decreased in all other counties in 2016, with the greatest decline recorded in Northeastern Estonia's Ida-Viru County.