The purpose of this study was to compare fluid flow rates across dentin surfaces treated with four conditioners. The effect of conditioning on the micro-shear bond strengths of glass ionomer cement (Fuji IX GP) and resin-based adhesives (Single Bond 2 or Clearfil SE Bond) were also investigated. Under a simulated pressure of 1.3 kPa, two dentin conditioners, phosphoric acid, and a self-etching primer were applied to the dentin surfaces. Dentinal fluid flows at baseline and after conditioning were recorded for 15 min each. The conditioned surfaces were examined using a scanning electron microscope. The micro-shear bond strengths of the glass ionomer cement and of the resin-based adhesives bonded to conditioned dentin surfaces were evaluated while simulated intrapulpal pressure was maintained at 0 or 1.3 kPa. Only the dentin surface etched with phosphoric acid showed a significant increase in permeability. Micro-shear bond strengths of Fuji IX GP were not affected by conditioning the dentin surfaces or by bonding at different intrapulpal pressures (0 or 1.3 kPa). The effects on bond strengths of resin-based adhesives depended on the system used. The simulated positive intrapulpal pressure during bonding significantly affected the adherence of Single Bond 2, whereas Clearfil SE Bond was unaffected.