[Chapter Abstract] This study applied the Quality Ratio (QR) index to integrate geochemical (TOC, fine grain content, and metal concentrations) and microbiological (Esterases (EST) and Dehydrogenase (DHA) activities of the in situ microbial community) parameters in order to classify the potential ecological risk of coastal sediments in dredging activities. Total concentrations (C) of Hg, Cd, As, Pb, Cr, Cu, and Zn (indicators of the complex mixture of contaminants in sediments) were determined in sediments inside Guanabara and Sepetiba bays (Rio de Janeiro, Brazil) and in oceanic dump sites outside the bays (C0) to calculate the contamination factor (CF = C/C0) and the degree of contamination (ΣCF). Likewise, DHA and EST activities were determined—respectively, biomarkers of energy production in the cell and hydrolase of organic matter outside the cell—which are altered under adverse conditions (e.g., contamination). The QR, a function of the microbial term DHA/EST and the geochemical term (TOC × ΣCF)/fine-grained content, was able to classify the sediments into three classes of risk: low (QR ≥  10−  1), moderate (10−  2 ≤ QR <  10−  1), and high (QR ≥ 10−  3). The QR was able to segregate the hot spots of contamination of the bays. The QR was also applied to an acute assay and successfully identified the microbial community shift under a contamination gradient when mixing with dredged sediments. Thus QR provides an accessible (low cost and fast) and efficient alternative for assessing both the quality of coastal sediments and the ex situ bioassays, as required by Brazilian legislation for dredging sediments, as well as for other developing countries.