The comparison of wet digestion and microwave digestion of Cd, Co, Cr, Cu, Mn, Pb, Zn, Fe, and Ni contents of the river bottom and sea floor sediments from the various locations of Turkey was performed in the present work. After digestions, the heavy metal concentrations were determined by flame atomic absorption spectrometry (FAAS). The heating programs for microwave digestion, different combinations, and volumes of acid mixtures were evaluated for microwave digestion efficiency. The studies in the present work show that the microwave-assisted digestions in closed system are easier and faster than the wet digestion. Also the results found by the microwave and the wet digestions were reliable and accurate. The procedures were also checked with two-stream sediment reference material (GBW 07309 and GBW 07310). Results for standard reference material (SRM) were in good agreement with certified values. The relative standard deviations for all metal concentrations were found to be lower than 10%.