A plume-scale mass balance is developed to assess the natural attenuation (NA) of dissolved organic contaminants in fractured, dual-porosity aquifers. This methodology can be used to evaluate contaminant distribution within the aquifer, plume source term, contaminant biodegradation and plume status. The approach is illustrated for a site on the UK Upper Chalk aquifer impacted by petroleum fuel containing methyl tert -butyl ether (MTBE) and tert -amyl methyl ether (TAME). Variability in site investigation data and uncertainty in the mass balance were assessed using probabilistic analysis. The analysis shows that benzene, toluene, m/p-xylene and o-xylene (BTEX) compounds are biodegraded primarily by denitrification and sulfate reduction in the aquifer, with an equivalent plume-scale first-order biodegradation rate of 0.49 a −1 . Other biodegradation processes are less important. Sorption contributes to hydrocarbon attenuation in the aquifer but is less important for MTBE and TAME. Uncertainty in the plume source term and site hydrogeological parameters had the greatest effect on the mass balance. The probabilistic analysis enabled the most likely long-term composition of the plume source term to be deduced and provided a site-specific estimate of contaminant mass flux for the prediction of plume development. The mass balance methodology provides a novel approach to improve NA assessments for petroleum hydrocarbons and other organic contaminants in these aquifer settings. Supplementary material: Plume organic chemistry, aquifer hydraulic conductivity and probability distribution functions used for mass balance inputs are available at https://doi.org/10.6084/m9.figshare.c.7016429 Thematic collection: This article is part of the Monitoring the aquifers collection available at: https://www.lyellcollection.org/topic/collections/monitoring-the-aquifers