Purpose: To evaluate the morphological changes in the acid-base resistant zone (ABRZ) at the resin/dentin interface after long-term storage in water. Materials and Methods: Two-step self-etching adhesive systems, Clearfil SE Bond (SE) and Clearfil Protect Bond (PB) (Kuraray Medical) were used. Human dentin disk sandwiches with resin composite were prepared, sectioned, and embedded in epoxy resin. The specimens were stored in water for 1 day, 1, 3 or 6 months, and then subjected to demineralizing solution and 5% NaOCl. The specimens were finally sectioned again, polished, argon-ion etched, and observed with SEM. Results: The outer lesion (OL) thickness at 1 day ranged from 10 to 15 µm but increased to approximately 30 µm after 6 months, suggesting gradual loss of dentin stored in water. A lower electron density was noted in the adhesives at the locations that were exposed to water. The ABRZs were observed clearly in all groups; the thickness of the ABRZ at the mid-point of the OL gradually decreased with time for SE. For PB, the thickness was stable up to 1 month, but decreased after 3 months. The bottom of the ABRZ in SE formed a right angle with dentin; in contrast, in PB, it sloped down toward dentin with a broadening bottom. Conclusions: Water storage resulted in changes both in the dentin substrate and the adhesive layer. An ABRZ was observed beneath the hybrid layer after long-term storage in water in both SE and PB. The ABRZ was thicker and relatively more stable in PB, probably due to fluoride release. Keywords: fluoride, acid-base resistant zone, recurrent caries, hybrid layer, self-etching adhesive system