Currently, only a few clear remains of Stone Age houses, revealed due to their sunken floors, are known to exist at four of the more than four hundred settlement sites of this period in Estonia. The focus of our paper is on three such hunter-gatherer settlement sites of the Narva and Comb Ware cultures, all located in different settings of the Baltic coastal zone. In order to analyse houses at these sites, archaeological collections and archival materials related to the Riigiküla I and Kõnnu sites were re-examined, and the site Jägala Jõesuu V is published here for the first time. Spatial analyses and a series of new radiocarbon dates let us to determine that three potential pit-houses at Kõnnu, dating to the first half of the 5th millennium calBC, and three pit-houses at the Riigiküla I settlement site, dating to the latter part of the 5th millennium calBC, belong to the Narva culture. Two new structures discovered during our analysis at Riigiküla I are related to the Comb Ware culture, along with the pit-house at Jägala Jõesuu V, from the end of the 4th millennium calBC. A comparison with the neighbouring territories shows that the Estonian coastal area forms the southern border of the distribution of pit-houses at least during the Narva and Comb Ware culture periods.