There are a variety of reasons why a well might need to be cleaned.
Bacteria. In the upper reaches of the well, and often extending deep into the water column due to pumping, the presence of oxygen encourages the growth of aerobic bacteria (bacteria requiring oxygen) and the oxidation of metals such as iron and manganese. Aerobic bacteria tend to cause clogging by the production of large amounts of slime and the entrapment of oxidized iron and manganese as well as other minerals such as calcite.
Debris from bacterial activity in the upper portions of the well tends to accumulate at the bottom of the well. Water in the lower portions of the well can become depleted of oxygen due to chemical reactions and bacterial activity, creating an environment for anaerobic bacteria (bacteria able to live without oxygen). These anaerobic bacteria, natural to the aquifer, are often responsible for methane gas, a fishy taste, various odors, and hydrogen sulfide (which causes a distinctive rotten egg odor). Aquifers, and therefore wells in them, may become anaerobic if hydrocarbons such as fuel oil or gasoline are spilled in them, and downgradient from uncontrolled trash deposits or manure piles. Such contaminant plumes will be preceded by increases in iron and manganese.
Many aquifers are naturally anaerobic, especially if hydrogen sulfide, methane, and carbon dioxide (derived from methane by bacteria) are present. Hydrogen sulfide and methane are common where there are oil and gas deposits, coal, and shale in the rock. Bacteria and other microbes known as archaeans generate hydrogen sulfide and methane as part of their metabolic processes. This kind of sulfide production is different from the process mentioned above. Microbes are versatile!
Sulfide corrodes steel and other metals and causes iron oxides and other minerals to deposit. Sulfide also combines with iron to form iron sulfides, which are hard and clog pores and fractures in rock, well screens, pumps, pipes and other equipment. Compounding these effects, sulfide oxidizing bacteria, which are aerobic, form spectacular light-colored slimes when they oxide the sulfide.
If nitrate is present in abundance, iron may also be oxidized (yes, without oxygen) and the iron oxides deposited. Often these processes occur together as the natural world works to reclaim your well.
Encrustation. This is the process by which a crust or coating is formed on the well intake and/or casing, typically through chemical or biological reactions. The cause may be chemical oxidation, such as that which usually forms calcite deposits, or it may be microbiological, as described. Such deposits may also trap fine sediment particles to form a weak “concrete.”
Fill-in: Over time, wells pumping from sand-containing aquifers may accumulate sediment in the bottom, closing off parts of a well screen or open borehole. Similarly, earthquakes or other vibration may cause parts of the well borehole to collapse, reducing capacity.