The Port of Tauranga plays a key role in New Zealand's export–import industry, and capital dredging commenced in October 2015 to extend the shipping channels to accommodate larger container vessels. This study investigated two-dimensional and three-dimensional subsurface estuarine sediment stratigraphy to predict the sedimentological conditions encountered during dredging operations to ensure that appropriate dredging methodologies were used to minimise the generation of turbidity. Eight cone penetration tests (CPTs), 14 core descriptions, and a high-resolution seismic investigation in Stella Passage (the main shipping channel of Tauranga Harbour) provided the basis for this research. Six major units comprise the stratigraphy; in ascending order they are lower pumiceous sand and silt (UNIT6), quartz-feldspar sand and silt (UNIT5), middle pumiceous sand and silt (UNIT4), silt–sand–clay (UNIT3), upper pumiceous sand and silt (UNIT2), and Holocene marine (UNIT1) sediments forming the modern seafloor. Three paleovalleys filled with sediments from UNIT2 were identified extending west to east across the channel. The CPT profiles were correlated with the seismostratigraphic units and their corresponding soil behaviour type to characterise each unit's sediment stiffness. The UNIT6 is unlikely to be encountered in current and future capital dredging operations because it is the lowest observed unit. A special dredging methodology may be required for UNIT5 and UNIT4 as they have high CPT tip resistance and undrained shear strength. For UNIT3, UNIT2, and UNIT1, which have very low CPT tip resistance and undrained shear strength, trailing suction and cutter suction dredging is appropriate. The potential turbidity of the water column, however, could impose a significant threat to marine biota and has to be taken into account.