This article describes a proposed work-sequence to generate accurate reservoir-architecture models, describing the geometry of bounding surfaces (i.e., fault locations and extents), of a structurally complex geologic setting in the Jeffara Basin (South East Tunisia) by means of geostatistical modeling. This uses the variogram as the main tool to measure the spatial variability of the studied geologic medium before making any estimation or simulation. However, it is not always easy to fit complex experimental variograms to theoretical models. Thus, our primary purpose was to establish a relationship between the geology and the components of the variograms to fit a mathematically consistent and geologically interpretable variogram model for improved predictions of surface geometries. We used a three-step approach based on available well data and seismic information. First, we determined the structural framework: a seismo-tectonic data analysis was carried out, and we showed that the study area is cut mainly by NW–SE-trending normal faults, which were classified according to geometric criteria (strike, throw magnitude, dip, and dip direction). We showed that these normal faults are at the origin of a large-scale trend structure (surfaces tilted toward the north-east). At a smaller scale, the normal faults create a distinct compartmentalization of the reservoirs. Then, a model of the reservoir system architecture was built by geostatistical methods. An efficient methodology was developed, to estimate the bounding faulted surfaces of the reservoir units. Emphasis was placed on (i) elaborating a methodology for variogram interpretation and modeling, whereby the importance of each variogram component is assessed in terms of probably geologic factor controlling the behavior of each structure; (ii) integrating the relevant fault characteristics, which were deduced from the previous fault classification analysis, as constraints in the kriging estimation of bounding surfaces to best reflect the geologic structure of the study area. Finally, the estimated bounding surfaces together with seismic data and variogram interpretations were used to obtain further insights into the tectonic evolution of the study area that has induced the current reservoirs configuration.