Radon is known as the main source of radiation for the general public. Results of extensive measurements of radon in water samples collected from private wells, natural springs and public water supply in Croatia are presented and annual effective doses are estimated. Measurements were performed by two different methods: the emanometry method (by using the AlphaGUARD instrument with additional AquaKIT module) and/or the liquid scintillation method (by using LSC TriCarb 2900). Water samples were collected in public water supplies in urban areas as well as private wells and springs in rural areas. The obtained average radon activity concentration based on the extensive measurement of almost 1000 water samples is 4.1 ± 1.9 Bq/l, with a minimum value of 0.2 and maximum value of 36 Bq/l respectively. The wide range of measured values is a consequence of the source of the water sample (ground/natural water versus treated water) as well as the geological structures around the water source. All estimated ingestion doses due to radon assuming consumption of 2 l of water per day from the observed source were within the interval 6.3–36.8 μSv (with calculated average and standard deviation 19.3 ± 10.3 μSv) for the water consumption from private wells and natural springs and 2.4–40.0 μSv (with calculated average and standard deviation 13.0 ± 10.5 μSv) for the water consumption from the public water supplies.