Atmospheric aerosols are often collected on substrates and analyzed weeks or months after the initial collection. We investigated how the selection of substrate and microscopy method influence the measured size, phase, and morphology of sea spray aerosol (SSA) particles and how sample storage conditions affect individual particles using three common microscopy techniques: optical microscopy, atomic force microscopy, and scanning electron microscopy. Micro-Raman spectroscopy was used to determine changes in the water content of stored particles. The results show that microscopy techniques operating under ambient conditions provide the most relevant and robust measurement of particle size. Samples stored in a desiccator and at ambient conditions leads to similar sizes and morphologies, while storage that involves freezing and thawing leads to irreversible changes due to phase changes and water condensation. Typically, SSA particles are deposited wet and, if possible, samples used for single-particle analysis should be stored at or near conditions at which they were collected in order to avoid dehydration. However, if samples need to be dry, as is often the case, then this study found that storing SSA particles at ambient laboratory conditions (17-23% RH and 19-21 °C) was effective at preserving them and reducing changes that would alter samples and subsequent data interpretation.