Vertical orthogonal joints are a common feature in shallow crustal rocks. There are several competing theories for their formation despite the ubiquity. We examined the exceptional exposures of orthogonal joints in flat-lying Ordovician limestone beds from the Havre-Saint-Pierre Region in Quebec, Canada (north shore of Saint-Lawrence River) to test conceptual models of joint formation in a natural setting. In the region, the spacing of cross-joints is consistently larger than the spacing of systematic joints by a factor of 1.5 approximately. The joint-spacing-to-bed-thickness ratios (s/t) are much larger in these beds (s/t = 4.3 for systematic joints, and 6.4 for cross-joints) than those in higher strained strata along the south shore of the Saint-Lawrence River (s/t = 1), highlighting the effect of tectonic strain in decreasing fracture spacing and block size. The high values of s/t indicate that cross-joint formation was unlikely caused by a switch from compression to tension once a critical s/t ratio for systematic joints was reached (as hypothesized in previous studies). We proposed a new model for the formation of orthogonal joint systems where the principal stress axes locally switch during the formation of systematic fractures. The presence of ladder-shaped orthogonal joints suggests a state of effective stress with σ1∗≫0 > σ2∗>σ3∗ and where σ2∗-σ3∗ is within the range of fracture strength variability at the time of fracture. This research provides a new mechanical model for the formation of orthogonal joint systems and cuboidal blocks.