Different and abundant suspended particles, from 10 to 50 μm, have been detected in the waters of an aquifer, observing various periods of fluctuation in the concentration of these particles that in some wells acquire a reddish colour. The morphology and mineralogy of the particles have been characterized by scanning electron microscopy equipped with X-ray detector and by X-ray diffraction. The isotopic composition of the carbonate fraction of the particles and the rocks surrounding the aquifer has been obtained by mass spectrometry. On the other hand, the isotopic composition (δ18O–δ2H and δ18O, δ34S of the sulphate in solution and δ13C DIC), electrical conductivity, Eh, and major ions have been determined in water samples from extraction wells. They are bicarbonate waters, with minor amounts of sulphates, chlorides, and dissolved nitrates. The solid particles are predominantly of authigenic origin (mainly magnesian calcite overgrown by fibrous aragonite cement), structures with diverse morphologies that have in common a high Fe content (spheroidal, filamentous, tubular or pellicular biofilms) and detrital grains (quartz, clays, and other aluminosilicates). The carbonate in solution is controlled by processes of bacterial sulphate reduction and oxidation of organic matter (induced by the accidental leakage of water with glucose subproducts into the aquifer, local anoxia, presence of sulphates and sulphate-reducing bacteria). The increase in water temperature in wells containing suspended particles, bad odours, negative isotopic compositions of carbonate in solution and positive isotopic composition of sulphate, and the decrease in pH detected during periods of precipitation of these particles are related to these processes. The Fe that caused the formation of red precipitates must come from the dissolution of the Fe conduits from a well. The pumping and the incorporation of Cl2O into the water (used to eliminate-oxidize organic matter) caused oxygenation and shift the balance of Fe towards the precipitation of oxides. The organic structures associated with the iron-rich precipitates are indicative of the activity of iron bacteria that caused the mobilization or precipitation of iron according to the redox potential and pH of the water.