San Pedro's main bus stop is outside the Catholic church. Buses leave hourly from 3am to 2pm for Guatemala City (Q60, four hours) and seven buses leave for Quetzaltenango (Q40, three hours) between 4:45am and 1:30pm…
From Pana Dock, boats to Panajachel (Q25) run every half hour or so from 6am to 5pm. Some go direct; others make stops at San Juan, San Marcos (Q10) and Jaibalito/Santa Cruz (Q20) en route.
Panajachel doesn't have a bus station per se, just this extended string of stops running west along Calle Real from the junction of Calle Santander.
Lanchas to Santa Cruz La Laguna, Jaibalito, San Marcos La Laguna and San Pedro La Laguna. The last boats tend to leave around 5pm.
Pick-ups stop for San Antonio Palopó (Q5, 30 minutes) via Santa Catarina Palopó.
Boats from San Pedro to Santiago (Q25, 25 minutes) run hourly from 6am to 4pm.
Lanchas to Santiago Atitlán. The last boats leave at around 5pm.