For roughly 20 years Water Well Pits have been outlawed on new well projects. A pit is generally a culvert, or wood/cement cribbing approx 4-8ft in diameter, and 8-12 ft deep. Once upon a time they served a purpose. To prevent the main water line from freezing, the well head would be 8 feet below ground level in a pit. The water line to the house (or barn etc.) would connect at this point to the water line down to the pump. At a depth of 8 feet below ground, with the aid of insulation, a heat lamp, and a cover, the risk of freezing would be greatly eliminated. Over time though, well pit construction can weaken, and surface water can enter filling up the bottom of the pit, and often enter the water well. The heat in the pit is also very inviting to rodents.
It is very common to enter a well pit and find mice, gophers, salamanders, or frogs. We've also found cats, weasels, and others. No skunks yet! Far too often the well head has no cover or seal, and the amount of surface water or rodent entry is anyones guess. Some of these pits are now so old and/or neglected that they are also a serious personal risk. Rotten wood in the structure or ladder has caused many injuries. The condensation that can build up in pits is very hard on fittings, control boxes, and pressure tanks as well. This can cause many problems and additional costs. Well pits can also be deprived of oxygen and can contain dangerous gases. People have died from these issues!
The government has been known to offer grants for well pit elimination, and are usually easy to obtain for farmers. An ideal upgrade would be to extend the casing to 2 feet above ground level, tie a pitless adaptor into the new casing, and connect to the existing underground water line. A pitless adaptor is simple yet very important and should be professionally installed. After these steps the well pit can be removed and/or filled in, and you will now have a nice looking well head with tight fitting cap. A pressure tank and control box set up in the house is the icing on the cake. It should be noted pits are still allowed to contain pressure tanks and control boxes, but it's not recommended.
It may be a good idea to install a hydrant before filling a pit, giving yourself a good water outlet near the well head.
For further knowledge- http://environment.gov.ab.ca/info/library/8197.pdf