The effectiveness of removing ammonium nitrogen from water by bio-filtration method with the use of nitrification beds has been assessed. The tests were carried out using four bioreactors with various fillings: diatomite, active carbon (WG--15), diatomite and sand, as well as diatomite and carbon. The paper analyses the effect of the character of external grain structure on the time of bio-film forming and on the durability of bonds of microorganisms with the carrier material, on the basis of changes in physicochemical parameters of the treated water, as well as scanning pictures of bio-film structure. The nitrification process was found to proceed with the highest effectiveness on two-layer (diatomite-and-carbon) and single-layer (diatomite) beds where the bio-film was most stable with consequential lowest turbidity of the treated water. The other finding was that the second phase of the nitrification process began earlier in two-layer filters.