Method for detecting, recovering, identifying and/or simultaneously enumerating bacteria and fungi, comprising: a) dissolving or suspending a nutritional mixture where bacterial and fungal growth is possible in a first solvent in quantities ranging from 1 to 50 g/L; b) adding one or multiple chromogenic, fluorogenic or bioluminescent enzymatic markers specific for a given bacterium or fungus, in quantities ranging from 0.01 to 2 g/L, to the dissolved or suspended nutritional mixture; c) absorbing the aforementioned components on one or multiple natural or artificial clay or ceramic three-dimensional structures with a specific surface of 2 x 10 3 to 6 x 10 8 m 2 /m 3 formed by a variety of nano-, micro- or macrocavities or their combinations; d) eliminating said first solvent; e) bringing said bacteria or fungi or the samples that contain it into contact with said three-dimensional structure in the presence of a second solvent that maintains the structures in conditions that ensure the growth and identification of bacteria and fungi during the decay of the markers inside the nano-, micro- and macrocavities of said clays or ceramics and over the surface of the structures; f) keeping the aforementioned at temperatures between 20 and 50°C for a period that coincides with the longest duration of the lag phase and the final growth acceleration phase of the bacteria and fungi with the slowest development in order to detect, identify and enumerate bacteria and fungi, wherein said nutritional mixture is selected from enzymatic hydrolysates of Spirulina platensis algae; extract of Saccharomyces cerevisiae obtained through enzyme hydrolysis and enzymatic hydrolysates of Torula fodder yeast; extract of sweet potatoes; tomato extract; enzymatic hydrolysates of beef heart tissue, of bovine blood and of beef liver; enzymatic hydrolysates of lactoalbumin from rennet whey, enzymatic hydrolysates or casein acids from buttermilk, and hydrolyzed or autolyzed from Eudrillus eugeniae; wherein said first solvent is distilled water or deionised water or aqueous salt solutions, alcohols and alcohol solutions, or dimethyl sulfoxide; wherein the second solvent is water, a hypotonic, isotonic or hypertonic solution of salts or the sample itself depending on the nature of those bacteria and fungi to be identified; wherein said one or multiple natural or artificial clay or ceramics three-dimensional structures are selected from kaolinite, halloysite, dickite, nacrite, chrysolite, antigorite, lizardite, vermiculite, mica, hectorite, saponite, hydrotalcite, muscovite, chlorite, diatomaceous earth, bentonites (montmorillonite, sauconite, beidellite, nontrolite), clinoptilotites, hydroxyapatites, zeolites and calcium phosphates, or their combinations; wherein said bacteria and fungi or the samples that contain them belong to a species, a genus, a group or a combination of these, including nanobacteria, bacteria, mould and yeasts, spores, hyphae or other propagules, and bacteria and fungi and samples that contain them, which can grow on the cited nutritional mixtures; wherein said bacteria and fungi are identified by visual or automatic detection of fluorescence; by the color change of the three-dimensional structure or of its consistency, texture, shine, opacity, tonality, homogeneity or transparency; or through the changes of color, shine, tonality, transparency or fluorescence of the second solvent or of the sample; or through the appearance of bioluminescence, both inside the cavities and over the surface of the structure; or by observing morphologic structures; or through metabolic reactions on the three-dimensional structure, in the second solvent or in the sample; or through a combination of some or all of the aforementioned identification methods and wherein said detection or determination of cell concentrations in the sample occurs through their visual or automatic enumeration over the surface of the three-dimensional structure, or by measuring the intensity of the fluorogenic, colorimetric or bioluminescent signal under ultraviolet, visible or infrared light, through electrical, thermal or magnetic signals, through pH changes, or by quantifying the emission or consumption of gases derived from the activity of bacteria and fungi during the lag phase or during the growth acceleration period, selected from carbon dioxide, oxygen, hydrogen sulphide, ammonia or hydrogen.