Subsurface remediation of groundwater and soils contaminated by chlorinated ethenes is a challenge as many sites remain with contaminant concentrations above regulatory limits. One issue that prevents site restoration is back diffusion of contaminants from low permeable layers into transmissive layers, which sustains contaminant plumes. In our research, we develop a two-dimensional analytical model of an aquifer-aquitard system which employs temporally variable boundary conditions to investigate the sensitivity of mass discharge across a downgradient control plane (DGCP) to both the mass discharge behavior from dense nonaqueous phase liquid source zones (i.e., the source-strength function or SSF) and contaminant mass stored in the aquitard. Existing models usually assume constant concentration boundary conditions which are not always representative of actual field conditions, especially when those boundary conditions are meant to represent the SSF. Modeling results are used to explore aquitard source functions, defined as the relationship between mass discharge across the DGCP and mass stored in the upgradient aquitard. We also explore the benefits associated with partial removal of DNAPL mass from the source zone, as well as the impacts of when those efforts occur in the lifetime of the source zone by testing the sensitivity of mass stored in the aquitard and mass discharge across a DGCP to different remediation scenarios. In instances where complete remediation is impractical, it is important for remediation managers (and other stakeholders) to know the options and expected results for partial remediation in the short term. Moreover, results are used to assess the relative importance of addressing contaminant mass in the DNAPL source zone versus the aquitard as the contaminant site ages. Finally, we explore a methodology for estimating contaminant mass in the aquitard with time, as a function of the SSF and mass discharge across a DGCP. This methodology complements site characterization efforts, especially at complex sites where detailed sampling of low permeable layers is a challenge.