Populations of sand flathead (once considered the most common fish in the Bay) and mud ghost shrimp (once the most common benthic organism in the Bay) both declined dramatically between the 1970s and 1990s. Although a study is underway to investigate if overfishing caused the flathead decline, there appears to have been no attempt to explain why the mud ghost shrimp became 700 times less abundant. Baykeeper has been looking into this in recent months. While there are no clear conclusions, some interesting observations have been made.
Firstly: while many scientific studies on different aspects of the Bay ecology at different points in time, there has not been ongoing monitoring of the bed of the Bay. What species live in or around the sediments and what chemical and physical changes are occurring? Without this info, any discussion on the health of the Bay is pure speculation.
Secondly: since the 1990s, the impacts of marine pollution in the Bay has been measured and discussed primarily in terms of potential risk to human health, with virtually no consideration to the impact on the health of marine species. You can read all about it here ongoing monitoring needed to explain species decline in Port Phillip Bay