Accurate particle size distribution (PSD) measurements of suspended particulate matter composed of flocs and aggregates are important to improve understanding of ecological and geomorphological processes, and for environmental engineering applications. PSD can be measured in situ (in the field) using a submersible sensor, or ex situ (in the laboratory) using samples. The methodological choice is often guided by logistical factors, and the differences in PSDs acquired by in situ and ex situ measurements are not acknowledged. In this study, a laser-diffraction instrument (LISST-200X) was used to compare in situ and ex situ PSD measurements. Samples measured ex situ were stored for three consecutive weeks and measured each week in a laboratory using different stirrer speeds. We observed that ex situ measurements display a higher D50 (median particle size) than in situ measurements of the same sample (up to 613% larger, 112% on average). Our experiments show that the difference between in situ and ex situ measurements can be explained by flocculation of the riverine sediments during the first week of storage. During the subsequent ex situ measurements, the stirring results in a significantly lower D50. Ex situ measurements are therefore unsuitable for flocculated suspended particulate matter. This study provides recommendations for optimizing PSD measurements by calculating the measurement times required to obtain robust PSD measurements (exceeding three minutes per sample), which are larger for field samples with coarser particles and wider PSDs.