San Carlos [1]’s half-dozen greasy hospedajes on the main drag charge as little as $3 per person, but you get what you pay for. If you’re short on cash, or just into slumming, try Hospedaje Peña (a block back from the water, tel. 505/2583-0298, $4 pp), a cheap but relatively secure dump with 10 rooms and streetside balcony.
A better bet is to walk 200 meters north of the bus station to Hotel Costa Sur (tel. 505/2583-0224, orlando104 [at] hotmail [dot] com, $7–12); rooms are clean and far quieter than the budget options in town. The owners can arrange day trips to Solentiname and other sites; they are part of a local tour guide effort and can recommend unique tours throughout the area.
Hotel Carelys (a half-block south of the park, tel. 505/2583-0389, $15) is also known as Aquiles or Doña Coco. Its 14 rooms are the cleanest and most pleasant in the city and include private bath, fan, and complimentary drinking water, and old magazines in Spanish.
Another popular choice is the Cabinas Leyko (two blocks west of the church, tel. 505/2583-0354, leyko [at] ibw [dot] com [dot] ni, $18–40). Its 22 somewhat damp and dark rooms start with a simple double with fan, but they have some higher-end alternatives with air-conditioning and cable TV as well—have a close look at the room first.
Links:
[1] http://www.moon.com/destinations/nicaragua/rio-san-juan/san-carlos