Methods are provided for making a reservoir-based sensor device. The method may include fabricating a first substrate portion which comprises an upper surface, an opposed lower surface, a plurality of through holes defining reservoirs between said upper surface and said lower surface, and a plurality of reservoir caps closing off one end of said through holes at said upper surface; fabricating a plurality of sensors on an upper surface of a second substrate portion; aligning the first and second substrate portions such that each of said plurality of sensors is in alignment with each of said plurality of reservoirs; and bonding together the lower surface of said first substrate portion and the upper surface of said second substrate portion to seal each of said sensors inside the reservoir with which it is aligned.