There are lodges on two rivers around Puerto Maldonado [1]: the Río Tambopata and the Río Madre de Dios. On both rivers, you will find a variety of accommodations, but for the most part, the jungle activities remain the same.
Links:
[1] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado
[2] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-tambopata-lodges/posada-amazonas
[3] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-tambopata-lodges/libertador-tambopata-eco-lodge
[4] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-tambopata-lodges/explorer-s-inn
[5] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-tambopata-lodges/the-tambopata-research-center
[6] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-tambopata-lodges/inotawa
[7] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-madre-de-dios-lodges/reserva-amazonica
[8] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-madre-de-dios-lodges/sandoval-lake-lodge
[9] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-madre-de-dios-lodges/casa-hospedaje-mejia
[10] http://www.moon.com/destinations/peru/the-amazon/puerto-maldonado/jungle-lodges/rio-madre-de-dios-lodges/heath-river-wildlife-center