Phytoplankton account for around half of planetary primary production and are instrumental in regulating ocean biogeochemical cycles. Around 70% of our ocean is characterised by either seasonal or permanent stratification. In such regions, it has been postulated that two distinct planktonic ecosystems exist, one that occupies the nutrient-limited surface mixed layer, and the other that resides below the mixed-layer in a low-light, nutrient-rich environment. Owing to challenges observing the planktonic ecosystem below the mixed layer, less is known about it. Consequently, it is rarely characterised explicitly in marine ecosystem models. Here, we develop a simple, two-layered box model comprising of an ecosystem (Nutrient, Phytoplankton and Zooplankton, NPZ) in the surface mixed layer and a separate one (NPZ) in a subsurface layer below it. The two ecosystems are linked only by dynamic advection of nutrients between layers and controls on light attenuation. The model is forced with surface light (modelled from top-of-atmosphere) and observations of mixed layer depth. We run our model at the Bermuda Atlantic Time-series Study site (BATS) and compare results with a 30+ year time-series of phytoplankton and nutrient observations. When compared with observations, the model simulates contrasting seasonal and interannual variability in phytoplankton in the two layers, lending support to the hypothesis that the euphotic zone of stratified systems can be described used two vertically separated planktonic ecosystems. Nevertheless, simulating the ecosystem in the subsurface layer was more challenging than the ecosystem in the surface mixed-layer, suggesting more work is needed to study controls on subsurface planktonic communities.