1) Why is it risky to go in the water after it rains?

Storm water runoff can pick up bacteria, fertilizers, oil, sewage, and other contaminants on its journey into our oceans and waterways. All that gunk hits the beach in a concentrated mass, before slowly dispersing out into the rest of the ocean. One study out of UC Irvine found that fecal indicator bacteria concentrations were 500% higher than bathing water quality standards following rain events in Southern California.

2) How long should I wait before it’s safe to go back in?

The Department of Environmental Health recommends avoiding activities such as swimming, surfing, and diving for 72 hours after it rains. Research has shown that the risk of infection is the highest during and the day after rain, and declines to around normal levels after three days.

More information at the link.