Australian ports serve diverse and extensive activities, such as shipping, tourism and fisheries, which may all impact the quality of port water. In this work water quality monitoring at different ports using a range of water quality evaluation indices was applied to assess the port water quality. Seawater samples at 30 stations in the year 2016–2017 from six ports in NSW, Australia, namely Port Jackson, Botany, Kembla, Newcastle, Yamba and Eden, were investigated to determine the physicochemical and biological variables that affect the port water quality. The large datasets obtained were designed to determine the Water Quality Index, Heavy metal Evaluation Index, Contamination Index and newly developed Environmental Water Quality Index. The study revealed medium water quality index and high and medium heavy metal evaluation index at three of the study ports and high contamination index in almost all study ports. Low level dissolved oxygen and higher level of total dissolved solids, turbidity, fecal coliforms, copper, iron, lead, zinc, manganese, cadmium and cobalt are mainly responsible for the poor water qualities of the port areas. Good water quality at the background samples indicated that various port activities are the likely cause for poor water quality inside the port area.