Plankton, at the bottom of the food web, play a central role in the entry of mercury into the aquatic biota. To investigate their role in mercury uptake, reliable analytical procedures for Hg analysis are highly sought. Wet digestion procedures for determining total mercury in different biological matrices have been established since years, however only few studies focused on planktonic samples. In the present work, a simple and cost-effective wet digestion method was developed for the determination of total mercury in samples of small plankton material using a cold vapor atomic fluorescence spectroscopy (CVAFS). The optimization of the digestion method was achieved by using glass vessels with Teflon caps, low amount of acids (3 mL w/w 65% HNO3 or 3 mL 50% v/v HNO3), a constant temperature of 85 °C, the presence and absence of pre-ultrasound treatment, and a continuous digestion period (12 h). Certified reference materials IAEA-450 (unicellular alga Scenedesmus obliquus) and BRC-414 (plankton matrix) were used to optimize and validate the digestion method. The recovery efficiency of the proposed method for IAEA-450 and BCR-414 (3.1 mg and 21.5 mg) ranged between 94.1 ± 7.6% and 97.2 ± 4.6%. The method displayed a good recovery efficiency and precision for plankton matrices of low size. Thus, allowing better digestion of planktonic samples for mercury analysis using CVAFS techniques.