Arabidopsis arenosa is the plant species closely related to widely known model plant A. thaliana and the model hyperaccumulator of Cd and Zn Arabidopsis halleri. A. arenosa occurs naturally both in diploid and tetraploid form, in contrast to A. halleri in which only diploid forms were found. The presence of diploid and tetraploid forms in A. arenosa may cause that selected populations of this species are capable of growing on heavy metal (HM) contaminated sites. Therefore, A. arenosa may be considered as very interesting research object of the mechanisms of HM accumulation and tolerance in plants. The aim of this study was to characterized the ecophysiology of several populations of A. arenosa from Central Europe. Sites with metallicolous (M) and non-metallicolous (NM) populations of A. arenosa were selected in Poland, Slovakia and Hungary. Populations in Slovakia and Hungary were selected on the basis of literature. Polish populations were selected on the basis of a preliminary research. The ploidy of each population were also taken into account. From each site 10 individual plants with soil samples were collected. Then plant and soil samples were acid digested in a microwave-assisted wet digestion system ETHOS1 (Milestone, Italy) and metal concentration was measured using flame atomic absorption spectrophotometer iCE 3500 FAAS (Thermo Fisher Scientific Inc., USA). Chlorophyll, anthocyanin and flavonol content were measured in situ on selected plants before their collection using Dualex Scientific+ (Force-A, France) sensor. The average annual temperature and precipitation values for the period 1982 to 2012 were determined using www.climate-data.org. The maximum value of chlorophyll content was observed in plants from Vernar (NM). The lowest value was recorded for metallicolous population from Bukowno (M). Moreover, a comparatively high chlorophyll content in the M population in Piekary Śląskie was also observed. The highest content of flavonols and anthocyanins were measured for populations from Miasteczko Śląskie (M) and Piekary Śląskie (M), which was positively correlated with the HM contamination of soil. The lowest content of both flavonols and anthocyanins were observed for populations from Szopienice (M) and Tematin (NM). The PCA analyses showed that populations grouped into five clusters: diploid populations inhabited warm sites (Hungary); tertraploid populations characterized by the low content of flavonols and anthocyanins; tetraploid M populations from Upper Silesia; tetraploid populations from nonmetalicollous but contaminated with HM sites; NM mountain populations from Slovakia. On the basis of the results of PCA analyses it is tempting to suggest that the climatic factors as well as ploidy level may determine the physiological status of plants. The increase of anthocyanin content seems to be the HM stress marker in situ. The increased content of flavonols may be related with a harsh environment. At the present state of investigations the changes in chlorophyll content seems to be not specific.