Seawater appears blue because it is a very good absorber of all wavelengths of light, except for the shorter blue wavelengths, which are scattered effectively.
The light attenuation is caused by the combined absorption and scattering properties of everything in the water, along with the water itself.
Changes in the sea’s color are primarily due to changes in the type and concentration of plankton.
Tropical oceans are clear because they are lacking in suspended sediment and plankton, which contrasts with the popular misconception that tropical waters have a high biological productivity.
In fact, they are virtually sterile compared with the cooler, plankton-rich temperate ocean regions. Inorganic particulates and dissolved matter also reflect and absorb light, which affects the clarity of the water.
The effect is caused by the selective absorption of light by water molecules, chiefly the oxygen component, that take out the red end of the visible light spectrum. In a similar way, ice masses at the poles and big icebergs look blue.
Reflection of light contributes to the color of the open sea, but does not determine it. Even pure water is slightly blue-green, because it filters out the red and orange content of light. However, impurities in seawater, especially organic substances, affect its appearance far more drastically.
In caves like those described, the light coming in must travel through a greater thickness of seawater than the light we usually see.
The strong absorption of wavelengths other than blue and green intensifies the ethereal effect.
In fact such light contains so little red that navy personnel who have been on submarine duty for several days find everything looks unnaturally ruddy when they return to the surface.
Blue Lake near Mount Gambier in South Australia is always blue, sun or no sun.
The lake is situated in a limestone area and is saturated with calcium carbonate. The color comes from the greater scattering of blue light by very fine particles of the compound suspended in the water.
Seawater is normally supersaturated with calcium carbonate, but magnesium in the water tends to stop it precipitating out. However, this can occur when seawater comes into contact with the calcium carbonate mineral calcite in rock or soil.
It is possible this what is happening in the caves of Malta.