Weedon Island Preserve's paddlecraft launch features a floating dock and small sandy beach located at the end of Weedon Drive NE, with a canoe washing station and restrooms nearby.

The South Paddling Trail, a marked 4-mile loop best paddled at mid to high tide, meanders through mangrove tunnels and seagrass flats; canoe and kayak rentals are available on-site through ECOmersion.

Parking is available during daylight hours only in designated areas, and the preserve prohibits overnight parking and combustion engines on the east side to protect the natural ecosystem.