Laguna de Apoyo
Take a taxi offered by the independent hotel, The Monkey Hut, for US$1 (if you have a booking there). See their website for information about pick up times and locations. You can also get a shared minibus from Hostel Oasis in Granada (US$3 November 2014), they run a couple of times a day - at 10am and again in the afternoon.
Another option for the independent traveller is by bus from Masaya. There are at least three buses a day, one very early about 6am, another at 10.30am and another mid afternoon. There are more frequent buses to the crater rim and you will need to walk (a long distance) down the hill or take a taxi. You can apparently walk from Granada cemetery in approximately 2-3 hours.
A taxi from Granada or Masaya should cost about US$10-15 (be prepared to bargain) and take about 30minutes.
This laguna is surrounded by mountains, as the laguna actually is within a crater of an inactive volcano. The water here is clear.
It is possible to go to the top of the mountains to a town called Caterina, there is a mirador here from here you can view the whole laguna.
The laguna itself is very isolated, and not many people come here. This is great, because you will feel like you are in your own little paradise.
Stay in Hotels
Rent Bikes from the Posada de la Abuela hotel
There are a few real estate plots around the river.
There are many small restaurants along the edge of the river. The most delicious is at the Hotel Posada de la Abuela
Either where you stay or there are a few comedors by the lake towards the Spanish School. The last one (not surprisingly) is probably the best and cheapest. Despite being in the middle of nowhere there are touts outside the first two, ignore them.
The juice at the Hotel Posada de la Abuela is fantastic!
There are two other more expensive options.