Chromium has garnered significant attention due to its classification as one of the most toxic heavy metals. It exists in two oxidation states: hexavalent chromium (Cr(VI)) and trivalent chromium (Cr(III)). Cr(VI) is soluble and highly toxic, posing a risk of lung cancer upon inhalation. On the other hand, Cr(III) exists in a precipitate form and is less harmful, even essential for mammals. Industries such as chemical pigmenting, textile tanning, metallurgy, and electroplating produce substantial quantities of hexavalent chromium, leading to the open dumping of chromium-contaminated sludge. When rainfall water infiltrates through these landfills, a leaching of contaminants occurs, potentially contaminating water bodies such as surface streams and aquifers. To counteract this, it is essential to design properly engineered bottom liner systems for landfills, particularly under saturated conditions. Bentonite clay has emerged as a widely used advective and diffusive clay barrier due to its remarkable swelling and adsorption capacity. In this study, numerical simulations utilizing FEM-based software were conducted by employing the steady-state moisture distribution in advective–diffusive equation, considering nonlinear isotherm conditions. The aim is to assess transient contaminant patterns beneath the engineered landfill. This study explored the impact of high concentrations and different adsorption behaviors, such as linear and nonlinear, under variable leachate head conditions on concentration, breakthrough time, and advective and diffusive flux beneath the clay liners system in a comprehensive manner. The results of the study demonstrate that advective flux is highly dependent on advective velocity, while diffusive flux is influenced by concentration differences concerning depth. Traditionally, the approach has been to assume linear adsorption, leading to an overestimation of chromium retardation at elevated concentrations. Therefore, it becomes crucial to consider nonlinear adsorption in the contaminant transport model to predict more accurately the practical behavior of chromium in such scenarios.