Local geological and tectonic processes have been pivotal in shaping the diverse sedimentation patterns observed in Jordan, forming sub-basins characterized by elevated organic matter content (TOC). This study aims to characterize the Maastrichtian basin, focusing on sedimentation rates using calcareous nannofossils and understanding paleoecological and paleo-oceanic conditions. It offers insights into the paleoenvironmental factors impacting oil shale deposition in the late Maastrichtian–Paleocene period. It employs classical biostratigraphical, semi-quantitative, and statistical methodologies to achieve its objectives of age determination and paleoecological insights. A total of 116 smear slides from two sites were obtained: the first, consisting of WA-1 (23 samples), WA-2 (18 samples), and WA-3 (11 samples), and the second, with 60 samples. Notably, the sites exhibit varying topography. WA-1 and WA-2, situated at lower elevations, have the highest Total Organic Carbon (TOC) levels, while areas with higher elevations in section four are visually identified by a light color. The study revealed varying patterns of calcareous nannofossil richness in the two investigated sites. These patterns were instrumental in defining biozones, with the utilization of marker species such as Lithraphidites quadratus, Micula murus, Micula prinsii, and Cruciplacolithus tenuis. Chronologically, these sections were classified as Maastrichtian–Paleogene, encompassing the following biozones in sequential order: UC-20a, UC-20b, UC-20c, UC-20d, and NP-2. Furthermore, the study identified two hiatus intervals, observed in sections WA-1 and KAS-1. The absence of certain biozones in the analyzed sections suggests that these sections correspond to distinct geological blocks within the basin, underscoring the role of tectonic forces during the deposition period. The sedimentation rate initially commenced at low levels but gradually increased due to topographic alterations. Notably, the biozone UC-20c demonstrated a clear trend toward warming and enhanced nutrient availability. In this context, the abundance and diversity of species were associated with increased continental influx into the sub-basin, resulting in rising nutrient levels and the number of calcareous nannofossils. This study enhances the understanding of the local and global effects such as tectonic and climates of the continuity of basins by deciphering calcareous nannofossil patterns and their correlation with sedimentation factors.