Soil is not “dirt” because of the inherent arrangement of organic matter, mineral, air and solution in a soil system. The organization of components in a soil generate a system conducive to plant growth, suitable to the construction of buildings and highways, amenable to waste disposal, active for water filtration and other functions that are beneficial to humans and the environment. We will highlight some of our past and on-going research activities involving microorganization in soils and micromorphological techniques to emphasize the importance of organization of soil components in microenvironments to understand soil formation, agriculture, forestry, remediation of contaminated soils, archaeology, and other disciplines. For example, we combine molecular technique (rDNA sequence) and mineralogy to ascertain the formation of calcium oxalate (whewellite), accumulation of quartz, oxides and 2:1 phyllosilicate on the thallus of various lichen colonies growing on basalt surfaces. In another study, we observed that secondary accumulations of 2:1 clays minerals are found in Aspicilia caesiocinera (Nyl.ex Malbr.) Arnold while oxides of manganese are associated with Xanthoria elegans (Link) Th.Fr. indicating that formation of specific minerals maybe restricted to certain species of lichens. We used x-ray computed tomography to track the changes in pore distribution in forest soils due to soil compaction by heavy harvesting machinery. A good understanding soil environments coupled with the use of X-ray absorption near-edge spectroscopy allows us to understand that Brassica juncea, a hyperaccumulator used in phytoremediation of chromium-contaminated soils, is able to tolerate high levels of metals because of its ability to store chromium in epidermal and cortical cells in the roots and epidermal and spongy mesophyll cells in the leaves. Water stable soil aggregates obtained from long term field experiments manifested a higher increase in soil physical quality (aggregate intra-porosity and shape-mammilated) in rainfed conditions at fallow parcels than medic cultivation. Further, thin section when combined with image analysis is an effective tool to compare the effect of different irrigation practices on the physical quality of soil. To address the dynamic nature of soil systems, we used micro-suction cups installed in a mini-rhizotron to determine the spatial variability in soil solution chemical composition due to ectomycorrhizal association. We have conducted archaeometric studies on the structural microorganisation of soil/artifact materials with dense distribution of small ruminant bones in dwelling layers/floors in serving archaeology for determining household customs in and around excavation sites. Moreover, when micromorphological techniques are combined with archaeometry, we are able to propose that the ‘stress coatings' and crystallinity of pseudowollastonite on shards of ceramics from the Neolithic Çatalhöyük archaeological dig to the Iznik of the Byzantine/Seljuk/Ottoman, as well as the exfoliated amphiboles and pyroxenes of the basaltic ceramics of the Hittites, may be evidences of the temperature fluctuations taking place during firing, whereas the illuviation coatings on the Çatalhöyük shard of rim may serve as clue for the short-term climatic fluctuations in Central Anatolia during the Holocene.In a related study of Bushman art from South Africa,the presence of 2:1 clays in pigments may indicate the use of clays as binders for paint pigments. In civil engineering, the formation of needle-shaped calcite and etringite in microcracks improved the strength of cements from blended fly-ash silica fume or slag-silica fume. Micromorphological study of ancient seeds of indigenous cereals and stones of ancestors of world olives is highly promising in revealing biological processes taking place within their decomposed/reshaped microstructure. From our results, we urge micromorpholgists not to limit themselves to techniques and should focus on understanding the implications of arrangement of organic, mineral and pore spaces to understand the basic processes (i.e., precipitation and dissolution, removal and addition, oxidation and reduction, complexation and acid-base reactions) in soil systems.