This is an article by our friend Phil Falcke who is currently studying a Bachelor of Science at Monash Uni.
Industrial-scale fishing is pushing most of the world’s fish stocks beyond the ability to cope.  All indicators suggest that most, if not all of the world’s fisheries are heading towards rapid collapse and extinction. In addition to mass removal of fish from our oceans’ ecosystems, we are selectively removing the larger predator fish at the top of a food chain that feed on smaller fish lower on the food chain.  When all these larger fish are used up, we move to the smaller fish, a process known as “fishing down the food chain”. Removal of the top predators in an ecosystem has cascading effects down the food chain. Numbers of prey that predators use to feed on can increase in number, reducing on the prey beneath them. This effect reaches all the way down the food chain to the aquatic algae, plants and photosynthetic bacteria that ultimately produce the food to sustain an ecosystem. Not surprisingly then, the absence of predators can cause collapse in food chains and ecosystems.
Reducing the population sizes of select fish species can also have genetic consequences.  Smaller population sizes of fish lead to increased inbreeding, reducing their genetic diversity.  Lower genetic diversity reduces the fitness of the fish, increasing the development risk of physical defects, sickness and disease.  Once small enough in number, species can enter what is called the downward “population spiral”, where lower populations of species reduce the physical fitness of individuals, leading to increased death and lower rates of breeding, and so on.  Once the spiral has been entered into, it is extremely difficult for a species to recover.
Some solutions have been proposed, for example, eating only herbivorous fish from the bottom of the food chain (This minimizes impacts on the food chain), and setting up of marine reserves to increase sustainable breeding populations of fish.  However, there are problems with the solutions offered.   It is extremely difficult to change human eating behaviour (think about how much you love tuna).  It is also doubtful that placing bans on the extraction of certain fish will help, as this leads to price hikes which fuel an already flourishing illegal fishing trade.  The effectiveness of marine reserves has yet to be demonstrated effectively.
It is clear though, that the main problem is gross over-extraction and over-consumption, driven by the demand and sale of fish.  As a planet, we need to drastically reduce the amount of fish we eat, especially while we try to figure out how we can fish sustainably, and while fish populations recover.
To get a good understanding of the fishing debate, this scientific journal article by Daniel Pauly and others is well-worth getting to know:
http://www.nature.com/nature/journal/v418/n6898/full/nature01017.html

The Australian Marine Conservation Society has released a guide to choosing fish from sustainable populations, and is a great step in the right direction:

http://www.amcs.org.au/default.asp?active_page_id=1
There is a great podcast from The Science Show on ABC Radio National. It’s called, “Will there be any fish left in 2050?” available from the itunes store (under podcasts).