This organosulfur compound is effective in inhibiting algae, fungi and bacteria, most notably the sulfate-reducing Desulfovibrio species. Since it is a competitive inhibiting microbiocide, it inactivates the electron transfer cytochromes of the microorganism. The thiocyanate fragment, NCS-CH₂-SCN, of the methylene ester of thiocyanic acid reacts to block the transfer of electrons in the microorganism, resulting in cell death.

Although methylene bisthiocyanate is a very effective microbiocide in industrial water systems, it is not very soluble in water and, therefore, is usually formulated with dispersants or supplied as a water slurry. The dispersants enable it to function as an effective microbiocide throughout the water system and enhance its penetrability of algal and bacterial slime layers.

Methylene bisthiocyanate is pH sensitive and rapidly hydrolyzes in pH ranges above 8.0. For this reason, it is not recommended for use in systems where the recirculating water pH generally exceeds 8.0.