Inks intended for use with fountain pens are water-based. These inks are commonly available in bottles. Plastic cartridges came into use in the 1960s, but bottled inks are still the mainstay for most fountain pen enthusiasts. Bottled inks usually cost less than an equivalent amount in cartridges and afford a wider variety of colors and properties.

As fountain pens are not tightly coupled with their inks as is with ballpoints or gel pens, some care must be taken when selecting an ink. Contemporary fountain pen inks are almost exclusively dye-based because pigment particles usually clog the narrow passages.

Traditional iron gall inks intended for dip pens are not suitable for fountain pens as they will corrode the pen (a phenomenon known as flash corrosion) and destroy the functionality of the fountain pen.^[67] Instead, modern surrogate iron gall formulas are offered for fountain pens. These modern iron gall inks contain a small amount of ferro gallic compounds, but are gentler for the inside of a fountain pen, but can still be corrosive if left in the pen for a long period. To avoid corrosion on delicate metal parts and ink clogging a more thorough than usual cleaning regime – which requires the ink to be flushed out regularly with water - is sometimes advised by manufacturers or resellers.

Some pigmented inks do exist for fountain pens, but these are uncommon. Normal India ink cannot be used in fountain pens because it contains shellac as a binder which would very quickly clog such pens.

Inks ideally should be fairly free-flowing, free of sediment, and non-corrosive, though this generally excludes permanence and prevents large-scale commercial use of some colored dyes. Proper care and selection of ink will prevent most problems.