It really depends on what you are tying to date. A simple method would be looking at the layers of sediment to look for identifing layers, such as ash from a volcanic eruption or silt from a flood. This would then be compared against existing records and possibly give a date.

However, the best option for an archaeologist would be the presence of organic material. Organic material can be radio carbon dated, although this can be trickier depending on the age of the remains as well as interference from radioactivity of the past 70 or so years. However, this is often how a site will be given a rough age.

Another way, if organic material cannot give a date, would be to look at the typology of artifacts present. Most artifacts can be dated off of style or material used. For example, in the region I have done work in, projectile points and pottery can give you a very accurate time frame of when a site was occupied. This is due to certain styles of points being used at certain times, as well as certain symbols and materials being used in the creation of pottery. This same manner can be used with essentially any artifact, although it is far easier to rely on when multiple can be looked at in this way, to rule out outliers.