I am guessing that letting the seawater in does decrease salinity. But I think it would be a complex system that also includes influxes of freshwater during wet periods. There will be a cycle balance that was achieved in the past between floods raising the water level and then opening the entrance to the sea, after which the lakes became and estuarine environment for a time. As the entrance silted up, the lake becomes different again. Somewhere in that cycle is probably the ideal environment for the weed growth in the Middle Lake.
It is frustrating that the monitoring station in the Middle Lake is out of action and has not been reporting salinity, turbidity, wind strength or water level since late last year. So now there is a big hole in the historical record just when it matters to us!
Links from here:
https://www.waterconnect.sa.gov.au/Systems/RTWD/SitePages/Home.aspx An example:
And Salinity Levels: