Permeability estimation in heterogeneous subsurface environments remains a significant challenge, particularly at municipal solid waste (MSW) dumpsites where material properties vary widely. This study compares permeability profiles obtained using cone penetration testing (CPT) and hydraulic profiling tool (HPT) methods at the Bhalswa landfill in Delhi, India. Six locations were investigated using both methods to evaluate permeability in waste, unsaturated, and saturated zones. Four different approaches were compared: correlation of permeability with soil behavior index (Ic) correlation and normalized cone parameters (Qt-Fr), and two HPT-based methods (in 2010 and 2021). Results showed that HPT methods provided more consistent permeability estimates in waste materials (10–5–10–4 m/s) where CPT measurements were erratic due to debris. However, in low-permeability clay layers, HPT methods overestimated permeability compared to Ic-based correlations (10–9–10–8 m/s). The Qt-Fr method and HPT-2021 correlation generally provided intermediate values with reduced scatter across different materials. The study demonstrates that combining CPT and HPT methods provides more reliable permeability assessment in heterogeneous materials, with method selection depending on material type and expected permeability range. These findings have important implications for contamination assessment and monitoring at waste disposal sites.