Beginning in 2014, golden algae blooms developed and released toxins into the water.
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The Rancho Santa Margarita Landscape and Recreation Corporation (SAMLARC) has tried various solutions to help improve the water quality.
SAMLARC's current approach is an aeration system that circulates the water and nearly two dozen floating plant islands which use the nutrients that would have otherwise fed the algae.
Lago Santa Margarita was recently stocked with about 1,000 bluegill and other small fish - a sign that bigger fish could be stocked as well.
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Officials are also replacing 11 million gallons of Lago Santa Margarita with freshwater to reduce salinity levels. The project should be completed by the end of July.
SAMLARC secretary Charles Villafana says the it means the private community lake could soon reopen for fishing.
"Hopefully by late fall, we'll have more catchable size fish and hopefully, by next year, we'll have a pretty thriving fishery again," says Villafana.