Membrane–water partitioning is an important physical property for the assessment of bioaccumulation and environmental impact. Here, we advance simulation methodology for predicting the partitioning of small molecules into lipid membranes and compare the computational predictions to experimental measurements in liposomes. As a step towards high-throughput screening, we present an automated mapping and parametrization procedure to produce coarse-grained models compatible with the Martini 3 force field. The methodology is general and can also be used for other applications where coarse-grained simulations are appropriate. This article addresses the effect on membrane–water partitioning of adding cholesterol to POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Nine contrasting neutral, zwitterionic and charged solutes are tested. Agreement between experiment and simulation is generally good, with the most challenging cases being permanently charged solutes. For all solutes, partitioning is found to be insensitive to membrane cholesterol concentration up to 25% mole fraction. Hence, for assessment of bioaccumulation into a range of membranes (such as those found in fish), partitioning data measured in pure lipid membranes are still informative.