Time of day. Early. The sound is glassy at first light, the sea breeze usually arrives late morning, and by mid-afternoon in summer you are paddling into a chop and watching thunderheads build inland. Sunrise on this water is genuinely worth the alarm.
Wind direction is everything. Across the sound, from the north or south, is fine: there is no room for a wave to build. Along the sound, from the east or west, is the one to check, because the channel gives wind a long run and the return leg becomes real work. Plan to paddle out into the wind and home with it.
Tide. The range here is small, but everything in the sound and bay ultimately drains through East Pass, so there is a current, and it is noticeable in the narrows and around bridges. Near the pass itself it is strong enough to be dangerous in a kayak. Paddle the sound and the bayous, not the pass.
Season. April, May, October and November are the best paddling months: warm water, settled air, thin crowds. Summer is hot enough that a midday trip is unpleasant and thunderstorms are routine after lunch. Winter gives you cold, still, empty mornings and the clearest water of the year, which is the trade-off many locals prefer.
The beach flags are not your rules, since they govern Gulf swimming, but a red flag on the island usually means a wind you will feel on the sound too.