In many circumstances, the ability to perform on-site, point-of-collection analysis can play a pivotal role in the goals or requirements of the inquiry. Toward this end, the use of commercial or customized kits, which require the analyst to manually perform the metering and mixing of reagents with the sample and the subsequent visual, spectrophotometric or other interpretation of the results, has become widespread. Often, these methods can suffer from poor reproducibility and sensitivity in addition to being tedious and time consuming. Flow analysis methods, such as traditional flow injection analysis (FIA) and the more recent sequential injection analysis (SIA), have found widespread use in the automation of sample and reagent handling and subsequent analysis for many important analytes. These methods can be completely automated and offer excellent reproducibility, minimized analysis time, and in certain configurations, very high sensitivity. We have developed a miniaturized, fully portable SIA-based instrument for on-site screening for chemical weapons degradation products during challenge inspections under the Chemical Weapons Convention, as well as for the sensitive analysis of other important environmental analytes. In this paper, we will discuss our portable SIA design, the analytical approaches utilized, and results obtained for the analysis of representative chemical weapons degradation compounds.