At the most simple level, navigation is accomplished through ideas known as dead reckoning and pilotage.
Pilotage is a term that refers to the sole use of visual ground references. The pilot identifies landmarks, such as rivers, towns, airports, and buildings and navigates among them. The trouble with pilotage is that often times, references aren't easily seen and can't be easily identified in low visibility conditions or if the pilot gets off track even slightly. Therefore, the idea of dead reckoning was introduced.
Dead reckoning involves the use of visual checkpoints along with time and distance calculations. The pilot chooses checkpoints that are easily seen from the air and also identified on the map, and then calculates the time it will take to fly from one point to the next based on distance, airspeed, and wind calculations. A flight computer aids pilots in computing the time and distance calculations, and the pilot typically uses a flight planning log to keep track of the calculations during flight.