Sea kayakers can visit many of the area's 48 islands, each with a unique habitat and ecology. Blue Waters Kayaking in Point Reyes offers classes, rentals, and tours that include moonlight paddles and camping trips. Tomales Bay is the largest unspoiled bay along California 's coastline and a popular destination for kayakers.

Kayakers can paddle along the forested hills and rock cliffs of Tomales Bay and along the Point Reyes National Seashore. Some of the bay's secluded beaches are only accessible from the water. Drakes Estero is a popular excursion for kayaking and wildlife viewing.