Unraveling structure-activity relationships is a key objective of catalysis. Unfortunately, the intrinsic complexity and structural heterogeneity of materials stand in the way of this goal, mainly because the activity measurements are area-averaged and therefore contain information coming from different surface sites. This limitation can be surpassed by the analysis of the noise in the current of electrochemical scanning tunneling microscopy (EC-STM). Herein, we apply this strategy to investigate the catalytic activity toward the hydrogen evolution reaction of monolayer films of MoSe2. Thanks to atomically resolved potentiodynamic experiments, we can evaluate individually the catalytic activity of the MoSe2 basal plane, selenium vacancies, and different point defects produced by the intersections of metallic twin boundaries. The activity trend deduced by EC-STM is independently confirmed by density functional theory calculations, which also indicate that, on the metallic twin boundary crossings, the hydrogen adsorption energy is almost thermoneutral. The micro- and macroscopic measurements are combined to extract the turnover frequency of different sites, obtaining for the most active ones a value of 30 s-1 at −136 mV vs RHE.