The aim of this study was to investigate fluid flow in dentin after restoration of carious teeth with resin composite bonded with a total-etching adhesive, with or without glass-ionomer cement lining. The roots of extracted third molars were removed and the crowns were connected to a fluid flow-measuring device. Each carious lesion was stained with caries detector dye and caries was removed using slow-speed burs and spoon excavators. Caries-excavated teeth were divided into two groups for restoration with resin composite bonded with a total-etch adhesive: (i) without lining; and (ii) lined with glass-ionomer cement before bonding. In non-carious teeth, cavities of similar dimensions were prepared, divided into two groups, and restored in the same manner. Fluid flow was recorded, after restoration, for up to 1 month. Caries-affected dentin was examined by scanning electron microscopy (SEM), and the bonded interfaces were observed using a confocal laser scanning microscope. No significant difference in fluid flow was observed between the two restorative procedures or between the carious and non-carious groups. The SEM images showed that the dentinal tubules of acid-etched, caries-affected dentin were usually still occluded, while some were patent. Limited penetration of fluorescent dye into dentin and into the bonded interfaces of restored carious teeth was observed.