To my knowledge there is no really complete manual including all the aspects of stream ecology. But there is two book which completely characterizes aspects of stream ecology:
1. Stream ecology: structure and function of running waters
JD Allan, MM Castillo - 2007
2. Stream Hydrology: An Introduction for Ecologists, Second Edition.
I too will recommend Stream ecology: structure and function of running waters
JD Allan, MM Castillo. I also suggest Methods in Stream Ecology edited by Hauer and Lamberti, 2007. Also on my shelf are two older but useful books: Fundamentals of Aquatic Toxicology: Effects, Environmental Fate, and Risk Assessment edited by Gary Rand, 1995 (more recent edition available?), and Restoring Streams in Cities: A Guide for Planners, Policymakers, and Citizens by Ann Riley, 1998.