Between October 20 and October 21, 1996, more than a foot of rain fell over Boston and poured into the Muddy River. Swollen by the deluge, the waterway overflowed its banks and spilled into the surrounding neighborhood, damaging the Museum of Fine Arts, Northeastern University and flooding the Green Line subway. Losses totaled some $70 million, and Green Line service was shut down for a week following the storm.

While Frederick Law Olmsted's design for the Emerald Necklace and Muddy River shaped the parks to contain floods and minimize damage, his ingenious design was discarded during the 20th century in favor of car-centric developments. Portions of the Muddy River were placed in underground pipes and paved over to make way for roads and parking lots. Ultimately, these pipes proved to be too small for heavy rain events like the one in 1996, and they backed up the river like a plug in a bathtub, leading to the extensive flooding seen.

With the vision of former Boston Parks Commissioner Justine Mee Liff, the Emerald Necklace Conservancy was founded in 1998 to advocate for the restoration of the Muddy River to its designed state. Work on the first phase of the restoration, which restored the river's above-ground course between the Riverway and Avenue Louis Pasteur, began in 2013 and finished in 2016. When the park was reopened in 2017, it was dedicated to Justine Mee Liff, who had passed away in 2002.