A rationale for the concept and strategy of monitoring of the atmospheric chemical composition and water quality are provided for manned spacecraft to be used for long-term and interplanetary flights. The main risk factors are formulated for a change in atmospheric and water composition during interplanetary space flights. A promising version of the analytical system for operational control of air and water quality in manned spacecraft is described considering these risk factors. Several gas analysis methods are proposed to be used in this system to partially overlap the nomenclature of detected species with respect to particularly important (critical) species. The water quality in the system is monitored by two instruments: one for measuring the total carbon content and the other for analyzing the ionic composition of water.