The health of freshwater aquarium fish and their breeding success depend critically on the quality of tap water. In general, tap water in Japan is potable, although the properties of tap water vary among regions in Japan. The city of Niigata is located in the largest rice production region of Japan. We have faced challenges concerning the reproduction of freshwater aquarium fish in Niigata. To determine whether water properties and quality affect the reproduction of aquarium fish in Niigata, we investigated the chemical properties of water and raised zebrafish in water from three different sources, namely tap water of Niigata in May, artificial freshwater (i.e., prepared via reverse osmosis), and natural spring water of Gosen, to document any effects on their sexual maturation and reproduction. We found that the tap water of Niigata was not stable throughout a year (median electrical conductivity = 147.1 μS/cm; SD = 25.6), with springtime lower than the first quartile. We also found that low concentrations of four pesticides in the tap water have been detected in May (max. concentration in 2020, bromobutide 2,000 ng/L, butachlor 600 ng/L, pyraclonil 200 ng/L, ipfencarbazone 20 ng/L). Moreover, rearing zebrafish in tap water negatively influenced both fish growth and reproduction: The sex ratio of adults was male biased (proportion of F0 male 70.8%); the average total length (30.5 mm) and weight (182 mg) of F0 males was decreased; the GSI of F0 females (9.7%) was decreased; the fecundity (the mating success 58.7%; the number of F1 eggs 63.1) of adults was reduced. Rearing in artificial freshwater could improve these outcomes (the sex ratio 55.7%; the total length of F0 males 31.8 mm; the weight of F0 males 211 mg; the GSI of F0 females 11.7%; the mating success 72.6%; the number of F1 eggs 99.0), whereas rearing in natural spring water from Gosen could improve the sex ratio (56.3%) and the weight of F0 males (200 mg), but not the others. Therefore, artificial freshwater made via reverse osmosis should be used for breeding freshwater aquarium fish in rice production region like Niigata. Finally, our results demonstrate that the reproduction of freshwater aquarium fish can serve as a bioindicator of low levels of organic pollutants in tap water and thus provide a basis for evaluating the safety of tap water for human consumption.