Three-dimensionally (3D) resolved ion trajectory calculations within the complex viscous flow field of an atmospheric pressure ion source are presented. The model calculations are validated with spatially resolved measurements of the relative sensitivity distribution within the source enclosure, referred to as the distribution of ion acceptance (DIA) of the mass analyzer. In previous work, we have shown that the DIA shapes as well as the maximum signal strengths strongly depend on ion source operational parameters such as gas flows and temperatures, as well as electrical field gradients established by various source electrode potentials (e.g., capillary inlet port potential and spray shield potential). In all cases studied, distinct, reproducible, and, to some extent, surprising DIA patterns were observed. We have thus attempted to model selected experimental operational source modes (called operational points) using a validated computational flow dynamics derived 3D-velocity field as an input parameter set for SIMION/SDS, along with a suite of custom software for data analysis and parameter set processing. Despite the complexity of the system, the modeling results reproduce the experimentally derived DIA unexpectedly well. It is concluded that SIMION/SDS in combination with accurate computational fluid dynamics (CFD) input data and adequate analysis software is capable of successfully modeling operational points of an atmospheric pressure ion (API) source. This approach should be very useful in the computer-aided design of future API sources.