Since the International Maritime Organization has paved the way towards zero emissions, more frequent applications of transition fuels in newly constructed ships have been observed. Fuels such as LNG or methanol are characterised by lower emissions when burned in engines. In order to diminish fuel consumption, and hence the rate of emission, support for the performance of a ship’s engines with energy from renewable sources such as photovoltaic (PV) installations is increasingly common. The efficiency of PV panels decreases with an increase in temperature, and it is therefore important to cool them. However, the cooling systems for PV panels impose additional financial outlays as well as a higher demand for electric power, which is needed to run the circulating pumps. A natural cooling process can occur in some vessels via high sea waves, when the ship’s decks are flooded by outboard water, although such cooling has an accidental and periodic character, as it results from weather conditions. Despite this, its potential demands a closer examination. This paper presents experimental research carried out with an experimental setup that allowed us to simulate the process of flooding of a PV panel with water waves of various frequencies, resulting from choppy periods at sea. Depending on the weather conditions and the character of flooding, our results indicate that an increase in the power of the PV module of about 18% is obtainable. Our research shows that when the intervals between flooding are longer, the periodic character of the temperature changes obtained by flooding the front surface of a PV panel with water is more distinctive.