Semiconducting transition metal dichalcogenide (TMD) thin films are promising candidates for high efficiency, large-area photoelectrochemical solar energy conversion devices. However, the efficiency of thin film TMD devices are usually much lower than the efficiency of bulk crystals. Due to the large variability in the physical dimensions of individual nanoflakes (e.g., area, thickness, shape, etc.), it is unclear how these differences affect the photocurrent generation of individual nanoflakes. Here we employ a single nanoflake photoelectrochemical approach to reveal the presence of both highly active and completely inactive MoSe2 nanoflakes. We observe, in the samples studied, that 7% of nanoflakes meet or exceed the efficiency of a bulk MoSe2 crystal. However, 66% of the nanoflakes are inactive. Additionally, photocurrent collection efficiency increases with nanoflake area and decreases more at perimeter edge sites than at interior step edges.