It’s wise to allow a full week for exploration of this region. Make your plane reservation from Managua [1] to San Carlos [2] early, as seats fill up fast. In general, expect about 25 percent higher costs for most goods in this isolated region (35 percent more on Solentiname).
Make use of your time in San Carlos to find updated boat schedules, make contact with downstream river lodges [3], and stock up on snacks and supplies.
Public transportation is both slow and capricious, but inexpensive. You are better off hiring a boat and driver or making arrangements with a tour company, which will affect your budget by an order of magnitude (organizing a group of like-minded travelers to share costs is one way to offset the price).
You could make it to Solentiname [4] and back in two days if the stars align, but boat schedules will make it more likely three or four. It’s only a day more to see El Castillo [5], which you should not miss. Don’t head farther downstream than El Castillo with fewer than four days including flights to and from the region.
Links:
[1] http://www.moon.com/destinations/nicaragua/managua
[2] http://www.moon.com/destinations/nicaragua/rio-san-juan/san-carlos
[3] http://www.moon.com/destinations/nicaragua/rio-san-juan/down-the-rio-san-juan/river-lodges
[4] http://www.moon.com/destinations/nicaragua/rio-san-juan/the-solentiname-islands
[5] http://www.moon.com/destinations/nicaragua/rio-san-juan/down-the-rio-san-juan/el-castillo