A multistage system and method for estimating respiration parameters from an acoustic signal. At a first stage, the method and system detect and isolate portions of the signal that exhibit long-term, moderate amplitude noise by analyzing cumulative energies in the signal, and portions of the signal that exhibit short-term, high amplitude noise by analyzing peak energies in the signal. At a second stage, the method and system filter heart sound from the signal energy envelope by applying an adaptive filter that minimizes the loss of respiration sound. At a third stage, the system and method isolate respiration phases in the signal by identifying trends in the energy envelope. Once respiration phases are isolated, these phases are used to estimate respiration parameters, such as respiration rate and I/E ratio.