Water is the reason this city is shaped the way it is, and it is also the part of a Miami trip most likely to be scheduled wrongly. The mistake is nearly always the same: the water goes in the afternoon, after a slow morning, because that is when a holiday day feels ready for it. In Miami that is precisely backwards.
Three things push everything afloat into the first half of the day. Lightning, which is the real one: Florida records more strikes than any other state, operators pull vessels for electrical activity rather than for rain, and in the wet season from roughly May to October the storms build through the middle of the day and open between about two and six. Wind and chop, which follow the same daily rhythm — the bay is at its flattest and clearest early, and by mid-afternoon the sea breeze has put a surface on it. And light, because shallow water only looks the way people imagine it when the sun is high enough to get into it but not yet bouncing off the top, which in practice means mid-morning.
The second thing to get straight is which body of water you are actually asking about, because there are three and they behave nothing alike. Biscayne Bay is the shallow, warm, protected sheet between the mainland and the barrier islands: sandbars, mangrove edges, flats, boat traffic and the best view of the skyline anywhere. The Atlantic, on the ocean side of Miami Beach, is open water with surf, no reef within swimming distance and the city's best swimming beaches. The reef is neither of those. The living reef tract lies offshore and to the south, and the serious snorkelling out of Miami means a boat — off Key Biscayne, or properly in Biscayne National Park, which is roughly 95 per cent water and reached from Convoy Point near Homestead, about an hour south of downtown. Nobody swims out to a reef from Miami Beach sand, because there is not one there.
Third, and specific to this city: check which side of the bay your boat leaves from before you book it. Departures run from the downtown waterfront, from marinas on Miami Beach, from Haulover, from Key Biscayne and from Homestead, and turning up on the wrong side of Biscayne Bay for an 8:30am departure is an hour you cannot get back.
The last section covers Florida's personal watercraft law, which is stricter than visitors assume and turns people away at the counter every day.