The influence of mercury on the transformation processes in the waters and the sediments in the reservoir of a small hydroelectric power plant (SHPP) Lakatnik was simulated in laboratory conditions. SHPP Lakatnik is the first (of nine similar) SHPPs put into exploitation in the middle part of the Iskar River (Bulgaria). In previous studies of the sediments in the reservoir of SHPP Lakatnik, our team found high concentrations of mercury, sometimes exceeding maximum concentration limit (MCL). In model bioreactors we studied the effect of mercury on the dynamics of the following hydrochemical and microbiological indicators: NH4
+, NO3
−, NO2
−, PO4
3−, chemical oxygen demand (COD), total organic carbon (TOC); aerobic and anaerobic heterotrophs (AH and AnH), Pseudomonas spp. (Ps.), Acinetobacter spp. (Ac.), sulphate-reducing bacteria (SR), denitrifying microorganisms (Dn). We looked for linear correlations among the studied indicators in order to find quick, mutual replaceability among them. The extent to which mercury affects the amount of key microbial groups and the rate of transformation of biogenic elements was calculated in percentages. The microorganism dynamics showed that AH, AnH and Ps. adapt more quickly and their number increased more in the presence of mercury, whereas SR, Dn and Ac. were inhibited to a greater extent by the presence of mercury. Mercury had a marked stimulating effect on Ps., which showed a 312% increase in number at the 192nd hour. The obtained results can be used when decisions have to be taken in risky situations related to increased concentrations of mercury in the sediments.