This resource contains a PCA2 grid for the greater Darwin Harbour region as part of a baseline seabed mapping program of Darwin Harbour and Bynoe Harbour. This project was funded through offset funds provided by an INPEX-led Ichthys LNG Project to the Northern Territory Government’s Department of Environment and Natural Resources (NTG-DENR) with co-investment from Geoscience Australia (GA) and the Australian Institute of Marine Science (AIMS). The intent of this program is to improve knowledge of the marine environments in the Darwin and Bynoe Harbour regions by collating and collecting baseline data that enable the creation of thematic habitat maps and information to underpin marine resource management decisions. The PCA2 grid was derived from a compilation of multiple surveys undertaken by GA, AIMS and NTG-DENR between 2011 and 2017, including GA0333 (Siwabessy et al., 2015), GA0341 (Siwabessy et al., 2015), GA0351/SOL6187 (Siwabessy et al., 2016), GA4452/SOL6432 (Siwabessy et al., 2017), GA0356 (Radke et al., 2017), and GA0358 and GA0359 (Radke et al., 2018), adding to those from previous surveys GA4425 and GA0333 collected by GA, AIMS, NTG-DENR and Darwin Port Authority.