<p>The migration of contaminants through inactive supply wells (ISWs) has drawn significant scrutiny because these wells can act as preferential flow pathways for contaminant transfer between aquifers. Declines in groundwater levels and clogging around ISWs can significantly reduce flow rates through these wells. Moreover, these wells can be surrounded by a finite-thickness skin, such as a gravel pack, and physical and biochemical clogs. Nevertheless, the impacts of fluctuating flow rates and the presence of a skin zone on contaminant migration through ISWs have not been exhaustively investigated. This study addresses this critical gap by initially fitting observational data from fieldwork carried out in California, USA, to characterize the variability in flow rates. Subsequently, a semi-analytical model incorporating both variable flow rates and skin effects was developed to elucidate contaminant migration. When benchmarked against a numerical solution, the approach exhibited superior accuracy and robustness. Several noteworthy findings emerged. First, the proposed exponential function precisely captures the variability in flow rates. Second, even minor alterations in the power index <i>λ</i> lead to substantial changes in breakthrough curves (BTCs), underscoring the high sensitivity of contaminant migration to variable flow rates. Third, increased dispersivity or reduced effective porosity within the skin zone accelerates contaminant migration. Furthermore, the contrast in dispersivity between the skin and aquifer leads to sharp changes in the spatial distribution of contaminants at their interface, which affects contaminant migration potential. Thus, variations in flow rates and skin effects profoundly influence contaminant migration through ISWs and must be rigorously considered in cross-contamination assessments.</p>