The red Noctiluca simulator describes ecophysiological processes of red Noctiluca scintillans within a 1-D water column. The total mixed layer depth (MLD) is divided into 1 m depths with vertical eddy diffusion between the blocks and across the ergocline; the latter describes movements into and out of the lowest block of the mixed layer depth. The mixed layer depth can be altered to represent nearshore (e.g., 5 m) to offshore (e.g., 30-50 m) coastal waters. For further details about the simulator and the operation manual please see: Mitra, A. (2025). Developing a simple digital twin of red Noctiluca scintillans. Zenodo. https://doi.org/10.5281/zenodo.16933559 Mitra, A. (2025) Red Noctiluca Simulator: Operation Manual. Zenodo. https://doi.org/10.5281/zenodo.16933521