Port Phillip is the largest enclosed seawater embayment in the Southern Hemisphere, more like an enclosed 'sea' than what is commonly thought of as a bay. The bay is over 1950 km2 in area and stretches 58 km from north to south and 41 km from east to west at its widest point. Its coastline is 264 km long, and the water catchment feeding the bay is 9790 km2, with over 3.2 million people living in the catchment area. Overall, the bay is in relatively good condition despite the urbanisation of its catchment and particularly the intense development of the eastern shore. The western shore contains a number of significant wetland habitats of international importance.
The bay is like a saucer when viewed in three dimensions - that is, it has a very large surface area relative to a very shallow depth (a maximum of only 24 m), with the deepest parts skewed towards the eastern side. This large surface area-to-volume ratio and the extreme narrowness of the outlet to the open seas (the 'Heads' between Point Nepean and Point Lonsdale through which the 'Rip' flows) are the prime determiners of its unique ecology.
Only 4% of the outside waters mix with those of the bay, hence its enclosed nature and shallowness - nearly half the bay is less than 8 m deep. Port Phillip Bay is generally cleaner and healthier than other comparable bays near major cities around the world. This condition is partly caused by the diversity of plants and animals found in the bay (over 1000 species) and in particular because of the way they interact. Toxicant levels are not generally dangerous and are decreasing, and eutrophication is not a problem because nitrogen and phosphorus levels are low, despite the inflows of various rivers and creeks and of the Western Treatment Plant (formerly the Werribee Sewage Farm). Ecological processes occurring on and about the sea floor are critically important to the health of the bay and heighten the need to avoid practices detrimental to the sea floor, such as the introduction of non-endemic species through ballast water.