With regard to the Water Framework Directive (WFD) and the required investigation of the whole water sample including suspended particulate matter (SPM), a storage stability study was conducted to determine the suitable storage time and conditions of 21 organochlorine pesticides (OCPs) spiked in water samples and pre-concentrated on solid-phase extraction disks (SPE disks). Furthermore, this work demonstrates the behaviour of three different certified sediment reference materials (CRMs) contaminated with OCPs in water samples as well as loaded on SPE disks under different temperature conditions and storage time periods. Extracts collected on SPE disks were stored for 3, 14 and 30 days at both 4 °C and −18 °C in darkness covered in (a) freezer bags and (b) aluminum foil. With few exceptions the results of these tests demonstrate stability of OCPs up to 30 days at −18 °C. The recoveries for most substances range between 84% and 133%. Furthermore, the stability of OCPs in water samples additionally spiked with CRM up to 500 mg and stored at a temperature of 4 °C in darkness up to 56 days was investigated. The addition of sodium azide enhanced the stability of some substances during storage, especially the endosulfans (I, II) but most substances were stable regardless of sodium azide addition over the entire storage period. An important conclusion of this study is that the storage of loaded SPE disks is an appropriate alternative to storing water samples.