Geophysical electrical resistivity surveys were carried out in a small lake named as “Nagi lake” located at Namthang, South District, Sikkim, India, for determining the source of in-situ seepage of lake water. Preliminary investigation suggests that the water seepage problem increased after the extension of the lake or after making a check dam surrounding the extended lake. The present study characterizes the origin of water seepage through an unknown fracture in the subsurface of “Nagi Lake.” Seepage path directions were demarcated with the help of an Azimuthal method, whereas sites of fractured areas causing lake water leakages were analyzed via Electrical sounding and profiling techniques. Maps of the fractured zone were developed with the help of a statistical analysis method, also known as the factor method of the traditional vertical electrical sounding (VES) that is ambiguous in method of curve matching. Main emphasis was given to locate subsurface fractures and their orientation. Delineation of location of subsurface fractures and their treatment will aid in minimizing the seepage of water from the lake. Retention of water throughout the year in lake will boost tourism near Nagi Lake area as well as aid in promoting water security in the region.