Rain clouds are typically 7,000 to 10,000 feet above the ground. Pilots at cruising altitude are unlikely to encounter heavy rain. Flying in the rain during severe thunderstorms and freezing rain, on the other hand, is difficult and sometimes dangerous. Visibility can be reduced by heavy rain.

The perception that planes "fly low" during rain is usually an observation of the approach and landing phase, rather than a change in cruising altitude. During rain, visibility is often reduced by low-hanging clouds and mist, requiring pilots to follow Instrument Flight Rules (IFR). To maintain a safe visual connection with the runway during the final stages of landing, Air Traffic Control may guide aircraft to lower altitudes earlier than they would on a clear day. Additionally, "low flying" is often a result of pilots wanting to avoid the most turbulent parts of a storm cell; if the heavy rain is concentrated in higher clouds, they may fly at a lower, more stable altitude to ensure passenger comfort. In 2026, modern avionics allow for "Category III" autolandings in zero-visibility rain, but human pilots still prefer to descend to a level where they can clearly see the "Rabbit" lights (Approach Lighting System). The "lower" appearance is also an optical illusion caused by the clouds being closer to the ground, making the plane seem much lower relative to the grey sky.