Great South Bay is a large, shallow coastal lagoon stretching approximately 45 miles along the south shore of Long Island, protected from the Atlantic Ocean by the barrier island of Fire Island. Its average depth is about 4 feet, with a maximum depth of 20 feet, creating generally calm conditions though wind-driven chop can develop. The bay is accessible through numerous formal boat launches, including Captree State Park, Heckscher State Park, Tanner Park in Copiague, Venetian Shores Park in Lindenhurst, and Smith Point County Marina in Shirley. Many of these are hard-surface ramps with parking for cars and trailers, though fees or permits are often required. Kayakers can also access the bay via rivers like the Connetquot and Carmans, which offer scenic marshland paddling before opening into the bay.

Tidal currents are a significant factor for trip planning, with strong currents reported, particularly near the Captree area and bridges. Paddlers should time crossings and longer journeys with the tide, aiming for a flood (incoming) tide to assist travel toward the mainland. The bay experiences a mix of conditions; it can be glassy and calm but also become choppy and "wonky" with opposing winds and currents. Exposure to wind across its broad, shallow expanse can create fetch, making conditions challenging for smaller craft. Motorboat traffic is present, especially in main channels and near inlets, so paddlers are advised to stay in shallower areas when possible for safety. The western entrance from the ocean at Fire Island Inlet may involve crossing active channels with boat traffic.

The paddling experience varies from peaceful, residential backwaters lined with expensive homes and canals to open bay vistas and natural marsh islands that serve as bird nesting sites. Wildlife includes osprey and seabirds. Water quality has faced historical environmental challenges, and conservation efforts are ongoing. For a multi-hour trip, a crossing from Jones Beach Island to Massapequa covers about six miles, while a paddle along the north side of Fire Island can be a 22-mile out-and-back journey. Early morning starts are recommended to avoid crowds and wind, and twilight paddles offer serene conditions with sunset views. All kayaks should be rinsed with fresh water after use due to the saltwater environment.