In this paper, we report new records of rare diatoms that have recently been found in Southern Poland. Planothidium nanum was found only in the upper reaches of the Centuria River, which is not exposed to human influence, while Navicula flandriae was found in two rivers (the Bolina and the Mleczna) affected by salt mine water from hard coal mines. The impact of anthropogenic salinity on diatom communities is as yet poorly documented. Therefore, we conducted a survey on this phenomenon. We surveyed seven sampling sites for diatom assemblages and habitat characteristics, including three sampling sites impacted by mine water. Navicula flandriae was recorded at both sampling sites affected by salt mine water and in two other rivers (the Centuria and the Mitręga), indicating its wide preference for salinity. We confirmed the occurrence of P. nanum at the same site where this species was found and described in our previous paper. In addition, we recorded the occurrence of this species at two other sites in habitats with similar characteristics (lower reaches of the Centuria and Wiercica rivers). Our results indicate a more common occurrence of N. flandriae and P. nanum, which means that further monitoring of diatoms is necessary