What kind for crops and irrigation crops are there in the area? Do they have a established riparian system? What other factors reducing water flow?
The problem is not the system, rather the demands upon the system. There have been attempts at establishing a system of runoff events, although, there really was never a natural system of flood events in the watershed to start with. Most of the bottom ecology was therefore shallow rooted and silty. The ony major flood events that occur in this area are landfalling hurrricanes, which average a hit once a decade (mean of every 7.4 years). The natural hydrology demands this slow release on the system followed by large purges....large releases of water will tend to favor organisms that are resistant to such force.... most of those being non-endemic to the area.
Add to that the high percentage of both sugar plantations and large tracts of central Florida dedicated to raising cattle, and you add a large amount of organic waste, and nitogenous base fertilizers, with phosphates added in. The St. Lucie River has times when it flows lime green from all the algal blooms, and is subsequently closed to fishing and other recreation.

It really is a matter of the overwhelming concentrations of both human and organic waste, ending up in a shielded lagoon with very little water swapping occuring between it and the ocean beyond.