Sodium azide, applied as microbial inhibitor, has caused unwanted by-products in environmental samples during anaerobic, long-term (2–3 year) experiments. When ignored, this can lead to the misinterpretation of observed phenomena. Sodium azide was indeed found to react with several components of environmental samples. Azide reacted with dissolved organic matter present in clay pore water, causing a lowered reducing capacity of the system. It also reacted with pyrite, forming thiosulfate and with ferrous iron, lowering its concentration in solution. When nitrite was added to the environmental samples, nitrous oxide and nitrogen gas were formed through reaction with azide. Azide could act both as an oxidant and reductant. Some of these reactions showed slow kinetics but nonetheless gave rise to significant amounts of by-products during these long-term experiments. When working with environmental samples, sodium azide can affect the chemical composition significantly, especially for long incubation periods. Other sterilization techniques such as filter sterilization are therefore advised.