Several stations around the city offer bus service to Managua. The most convenient is located half a block south of Parque Central on Calle Vega. The trip should cost $0.20  and take about an hour. This same bus will drop you on the outskirts of Masaya for half the price. Departures are every half hour between 4:20 a.m. and 6 p.m. Buses to Rivas, a transport hub that serves San Juan del Sur, leave from a station 3 ½ blocks south and one block west. Frequent departures between 5:45 a.m. and 3:10 p.m.
A company called Paxeos offers private shuttle buses to destinations around Nicaragua. Prices are steep, see their listing in the Tour Operators section for more details. TransNica has a station on Calle Tamarindo with departures to San Jose (Costa Rica) at 6 a.m., 8 a.m., and 11 a.m.
Granada is also served by a ferry that departs every Monday and Thursday at 2 p.m. It's a 3 ½ hour trip to Isla Ometepe, or a 14 hour trip to San Carlos on the far side of the lake, near the Costa Rican border. Tickets should be bought in advance from the ferry office at the end of Calle la Calzada.