Polymer elution from bentonite-polymer composite geosynthetic clay liners (BPC-GCLs) and the efficacy of using flow stress of polymer hydrogels as a screening tool were evaluated in this study using permeant solutions that alter hydraulic conductivity. For several of the BPC-GCLs that were tested, hydraulic conductivity increased during permeation, with polymer eluted in the effluent. BPC-GCLs with lower hydraulic conductivity (<10-11 m/s) produced smaller volumes of effluent with higher polymer content, whereas BPC-GCLs with higher hydraulic conductivity (>10-11 m/s) produced larger volumes of effluent with lower polymer content. Increases in intrinsic permeability were concomitant with increases in hydraulic conductivity, indicating that pore spaces opened as polymer was eluted. Opening of pore spaces was confirmed by macro- and microscopic imaging of flow paths and polymer arrangement. Flow stress of the polymers decreased with increasing moisture content, indicating that conditions that promote higher hydrogel moisture content are coincident with greater propensity for polymer elution. BPC-GCLs with polymers having higher flow stress had lower hydraulic conductivity, indicating that flow stress has potential as screening measurement for chemical compatibility of BPC-GCLs.