We study the effect of atomic-scale surface-lubricant interactions on nanoscale boundary-lubricated friction by considering two example surfaces-hydrophilic mica and hydrophobic graphene-confining thin layers of water in molecular dynamics simulations. We observe stick-slip dynamics for thin water films confined by mica sheets, involving periodic breaking-reforming transitions of atomic-scale capillary water bridges formed around the potassium ions of mica. However, only smooth sliding without stick-slip events is observed for water confined by graphene, as well as for thicker water layers confined by mica. Thus, our results illustrate how atomic-scale details affect the wettability of the confining surfaces and consequently control the presence or absence of stick-slip dynamics in nanoscale friction.