||According to European Union directives (WFD, 2000; GDD, 2006) the identification and determination of uncertainty - also this associated with sampling, preservation and transport of samples - is an important part of the overall groundwater monitoring effort. Moreover, directive (DT 2009) indicate necessity of implementation the quality assurance and quality control program (QA/QC) of research in water monitoring. They also give the limit of quantification threshold value, as a 30% or less of environment quality norms. Authors describe example of implementation of limit of quantification (LOQ) and practical limit of quantification (PLOQ) for the estimation of uncertainty involved in sampling and analytical processes during geothermal water monitoring from the Banska Nizna PG-P1 and PG-P3 wells. Physical parameters and chemical composition of geothermal waters can be changed during the long-term exploitation, so it is especially important to control quality of analyses (measurements), on the base of which we can confirm stability of the physico-chemical parameters.