The present study highlight the toxicity levels of different heavy metals in aquatic environment of one of the most polluted river of Mumbai-the Mithi River. Although the river has attracted tremendous attention after 26/7 flood in Mumbai, the pollution level of the river has remained neglected issue. The present study was performed for two assessment years 2009-10 and 2010-11 at three different sampling stations namely Airport, CST Kalina and BKC Taximen's Colony along the flow of Mithi River. The results of present investigation indicates that the concentration levels of most of the heavy metals like Al, As, Cd, Cr, Hg, Ni, Pb, Sr and Mn obtained during the assessment year 2010-11 was higher than that obtained during 2009-10 by the factor of 1.4 to 5.7 µg/L. The environmental impact of these toxic heavy metals is discussed. The results point out the need of rational planning of pollution control strategies, so as to keep check on release of toxic heavy metals in the river. It is expected that the present study will be useful for rational planning of pollution control strategies and their prioritisation; to evaluate effectiveness of pollution control measures already is existence and to assess the nature and extent of pollution control needed.