A study of the mineralogy, chemical composition and structure of poorly-crystalline saponite precipitated from a submarine hot spring in Eyjafjordur, northern Iceland is reported. Special emphasis was placed on the microstructures of the minerals and a possible connection with biological activity during their precipitation. The microstructures of the minerals were found to be very similar to specific clay minerals precipitated from geothermal vents in oceanic rift zones. The composition of the minerals was, however, found to be similar to magnesium silicate scales formed in geothermal installations in Iceland where geothermal waters were mixed with cold fresh waters. High contents of organic substances were found in the clay mineral samples as compared to geothermal precipitates from other localities. Microstructural features of the layer silicates in one of the samples suggest that a gelatinous substance was a precursor of the saponite clay. The organic matter content appears to be greater when the precipitates are more crystalline.