With the exception of the service between Panajachel and Santiago Atitlán, Lago Atitlán's public ferries have been replaced by private water taxis. Although they don't follow a schedule, the private boats are much faster and cost about the same. Panajachel has two primary docks, one at the end of Calle del Embarcadero and one at the end of Calle Rancho Grande. The first is for private boats on the San Pedro route, stopping at Santa Cruz, Jaibalito, San Marcos, Santa Clara, and San Pedro. It's about Q15, no matter where you get off.
The other dock is for hour-long journeys to Santiago, with departures at 6 AM, 8:30 AM, 9 AM, 9:30 AM, 10:30 AM, 1 PM, 3 PM, 4:30 PM, and 5 PM, and return trips at 6 AM, 7 AM, 11:45 AM, 12:30 PM, 1:30 PM, and 4:30 PM. The cost is about Q10. Private boats occasionally take passengers to Santiago in about half the time.