A flow-through monitor for detecting molecular contamination (MC) within a fluid flow. The monitor has a diffusion chamber having an inlet port and an outlet port, and a structure for supporting a fluid flow from the inlet port to the outlet port. The structure includes a flow gap causing a diffusion of molecular contaminants into the diffusion chamber, while substantially preventing, for a rate of the fluid flow above a predetermined magnitude, particulate contaminants within the fluid from entering the diffusion chamber. A SAW device detects molecular contamination interior to the diffusion chamber. Fluid input to the flow-through monitor may be diluted by a pure fluid for extended monitor life. A system for aggregate sampling connects an ensemble manifold upstream of the flow-through monitor. A system for triggered sampling connects a sample preconcentrator downstream of the flow-through monitor. A chemically selective membrane may be located between the flow gap and the SAW. A test surface adapted to collect MC and located to sample the same fluid as the SAW may also be combined with the monitor. A chemical filter and/or heater may be located upstream of the flow-through monitor and valved to the monitor alternately to the unfiltered and unheated sample.