A transport theory for atomic matter waves in low-dimensional waveguides is outlined. The thermal fluctuation spectrum of magnetic near fields leaking out of metallic microstructures is estimated. The corresponding scattering rate for paramagnetic atoms turns out to be quite large in micrometer-sized waveguides (approx. 100/s). Analytical estimates for the heating and decoherence of a cold atom cloud are given. We finally discuss numerical and analytical results for the scattering from static potential imperfections and the ensuing spatial diffusion process.