Real-time in situ atomic force microscopy (AFM) has been employed to examine the electrochemical nucleation of epitaxially oriented, crystalline monolayers of bis(ethylenedithiolo)tetrathiafulvalene triiodide, (ET)(2)I-3, on the basal plane of highly oriented pyrolytic graphite electrodes decorated with circular, single-layer-deep pits created by thermal etching. The nucleation of the monolayers in the pits is inhibited compared to the contiguous terraces. The time required for pit filling scales inversely with pit diameter, with nucleation completely suppressed in pits with diameters less than 100 nm. The suppression of growth in the pits can be attributed to the surface discontinuity created by the pit edge that prevents surface diffusion of ET growth units from the surrounding terrace to the pit. Consequently, growth of nuclei in the pits is limited by the amount of ET arriving in the pit by diffusion directly from solution. Numerical simulations of aggregate growth in pits illustrate the influences of transport and the finite boundary created by pit wall on the evolution of aggregate shape and size during growth, while revealing the most probable locations for nucleation within the pit. These studies illustrate the convenience of investigating nucleation processes triggered by electrochemically driven changes in redox state, the advantage of AFM for probing nucleation in the nanoscale-confined environments, and the role of transport in nucleation of ordered films.