A system 300 for the substantially-automated hybridization of a plurality of microarray slides. The system comprises an enclosure 310 with a wash basin 312 having an open top end, a lower carrier rotor 330 disposed within the wash basin on a support axle 318 for receiving a plurality of microarray slide substrates 362, and an upper clamp rotor 340 disposed above the lower carrier rotor on the support axle for receiving a plurality of disposable chamber assemblies 240. The system is further configured so that lowering the upper clamp rotor to engage with the lower carrier rotor couples the plurality of chamber assemblies to the plurality of slide substrates to form a plurality of sealed reaction chambers 244, and raising the upper clamp rotor to disengage from the lower carrier rotor de-couples the plurality of chamber assemblies from the plurality of slide substrates to unseal the plurality of reaction chambers.