Diatoms are unicelullar, eukariotic, photosynthetic microorganisms that live in most freshwaters, in a wide range of aquatic habitats. In terms of different pH values, different concentrations of dissolved substances and nutrients and also diverse temperature range. They indicate a change in the physical, chemical and biological environmental conditions as biological indicators and as such are used in the assessment of ecological status and monitoring of freshwater habitats, they greatly contribute to primary production. A electronic check-list database for freshwater diatoms was obtained after analyzing research field date in the period from 1998 to 2013 year. Conducted researches covered planktonic and benthic/ periphyton diatoms in the lentic biotope (natural lakes and accumulations) of Croatia: Baćina lakes, lake Butoniga, Plitvice lakes (Kozjak, Prošće), Visovac lake, lake Vrana in the Cres island, Vrana lake by Biograda na Moru, and accumulations on the river Dravi (Čakovec, Dubrava, Varaždin). Electronic check-list database combines basic informations for 303 species, 12 varieties and 1 form of diatoms grouped in 83 genera. Considering number of identified species at the study sites, dominante diatom group is bilaterally symmetrical Pennatae in which is the genera Navicula Bory as most represented in number of species and abundance per the number of cells. In Baćina lakes was determined the largest number of diatom speacies.