The distribution of the chemical species of the elements Al, Fe, Zn, Cu, Cd, and Pb in surface waters influenced by coal mining and coal processing industry in Bulgaria was calculated using two chemical equilibrium models—combined ion association—Stockholm humic model (IA-SHM) and biotic ligand model (BLM). It was established similarity in the results of the both models in water with dominant organometallic microelement species. When inorganic species (free ions, hydroxy, and carbonate species) were dominant, differences in species distribution were calculated, the largest for Zn, followed by Cd, Pb, and insignificant for Cu. These differences are due to the mutual competition of metals accounted for by IA-SHM, which makes it more effective for estimating microelement bioavailability. The results point to the absence of free ions of Al and Fe and the presence of insignificant amounts of Cu in all studied waters and of Pb in waters with low alkalinity, which defines a low level of bioavailability for these elements. High free ion contents were calculated for Zn and Cd, which makes them more bioavailable and therefore riskier for aquatic organisms despite their low concentrations. In highly alkaline waters, 15–40% of labile carbonate species of Pb were calculated, which, together with its high concentration, makes it the most hazardous element in these waters.