Marine dissolved organic matter (DOM) is one of the largest exchangeable organic carbon reservoir on the planet. The main proxy to track the distribution of DOM in the aquatic environments remains dissolved organic carbon (DOC). Thereby the optimal protocol for long-term DOC preservation in seawater samples must be defined. In this context, we monitored bulk DOC concentrations and its size class distribution in filtered seawater samples during yearlong experiments. With different conservation mode, we tested two types of commonly used materials (borosilicate brown glass and high-density polyethylene, HDPE) and three conditioning protocols (untreated, acidified at pH 2 and frozen at −20 °C). Offshore samples collected along the entire water column of the Pacific Ocean and stored in HDPE bottles were also analysed after 2 years of storage at pH of 2 and compared to frozen samples. Results demonstrated that bulk DOC concentrations can be accurately determined in untreated samples for one month and for years in frozen samples as well as in acidified samples, when samples are stored in acid cleaned HDPE bottles or flame sealed glass ampoules. Storage in brown glass vials with Bakelite caps seems more uncertain. The study of the size class distribution of DOC reveals the possibility to study DOM for 1 month in filtered samples with no additional treatment and for years in frozen samples when stored in acid cleaned HDPE bottles. Significant changes in DOC size fractionation were observed when samples were acidified. The high molecular weight (HMW) compounds and the humic substances from the upper 1000 m were significantly degraded at pH 2, incorporating DOC in the low molecular weight (LMW) fractions. These experiments provide preservation guidelines for future studies that aim either to study bulk DOC or the chemical properties marine DOM. It is recommended to store seawater in HDPE vials at −20 °C for DOM study, or at pH 2 for bulk DOC measurements.