From 30-31 March 1988, the Todd River catchment saw the largest rainfall recorded within 24 hours. More than 300 mm of rain fell in the western MacDonnell Ranges, with over 150 mm at stations further east, around Alice Springs. The flood reached a gauge height of 3.98 m.

The Todd River burst its banks, flooding large areas of Alice Springs, and isolating it from the south as road and rail links through Heavitree Gap were cut. Further south, the Hugh and Palmer Rivers also burst their banks, cutting the Stuart Highway.

The weather system which caused the flood resulted from the combined effects of two tropical depressions, one forming to the north-east of Darwin, and the second in the Indian Ocean south of Java. The combined depression then travelled in a south-easterly direction to Alice Springs.

Approximately 300 people were evacuated from low-lying areas, and there was considerable damage in the Alice Springs area. There were three fatalities in the floods.

The Insurance Council of Australia estimated the 1988 damage at $10 million, with the 2011 estimated normalised cost of $68 million.