In highly modified and managed systems the balance of freshwater inputs discharged to estuarine systems are important to maintain salinity balances and thus estuarine function. However, the availability of freshwater is highly dependent on upstream water management to provide flood protection whilst meeting freshwater demand for people and the environment. In South Florida, water is managed by a water control plan with Lake Okeechobee at the center. Currently, water levels within the lake are managed based on the Lake Okeechobee Regulation Schedule of 2008. The new regulation schedule, Lake Okeechobee System Operating Manual (LOSOM), updates water management rules while attempting to balance the needs of downstream systems; salinity and water quality in the Caloosahatchee and Saint Lucie (northern) estuaries; and more water for the southern Everglades. This study evaluates LOSOM relative to ecologically significant performance measures for the northern estuaries. Overall the proposed regulation schedule is expected to provide a more sustainable flow regime to the estuaries by reducing stressful and damaging discharge events. Moreover, new management rules combined with new infrastructure are expected to reduce low discharge events to the Caloosahatchee estuary and reduce stress on key indicator species such as Vallisneria americana during the wet season. This regulation schedule provides improved conditions for the estuaries, but Lake Okeechobee carries the burden. Future restoration and water management strategies are needed to maintain the benefits afforded to the estuaries while at the same time reducing the stress and damage to Lake Okeechobee to develop a more sustainable and resilient system.