A multiple channel site-isolated reactor system and method are described. The system contains a reactor block with a plurality of reactors. Input lines are coupled to each reactor to provide a fluid to the respective reactors. A sealing element associated with each reactor contacts a surface of a substrate disposed below the reactor block, which defines isolated regions on the surface of the substrate. A dissolution rate monitor extends into each reactor to monitor a rate of real-time dissolution of one or more layers on the surface of the substrate when it is disposed proximate to the surface of the substrate.