The predictions of the competitive exclusion principle about the number of coexisting species not exceeding the number of limiting resources in equilibrium constitute an ecological puzzle for phytoplankton ecosystems. Here we present a synthesizing unit (SU) based competition model taking co-limitation into account, which is the extension of the competition model developed by Dutta et al. (2014).The study aims at understanding the mechanisms of violation of competitive exclusion principle for phytoplankton species with seasonal environmental forcing when multiple resource limitation is taken into account and species growth is formulated based on SU. We also explore the role of changing environmental conditions on species coexistence on a seasonal and a decadal time scale by linking the model forcing to the Helgoland Roads Time Series data sets. For the first time, based on the Helgoland Roads data, we are able to find a realistic parameterization for the phytoplankton competition model where growth is formulated using SU concept. Our study confirms that more species than limiting resources can coexist with seasonal variations of environmental conditions. This supersaturation is related to periodic changes in species’ biomass, variation in interspecific competition and niche configuration, nonlinear functional response and the position of resource supply within the convex hull of species’ resource uptake rate. Changes in environmental conditions within realistic ranges do not prevent the coexistence of species rather it slightly changes species’ biomass and turnover time. This study also confirms that our model with SU based species growth performs better than species competition model where multiple resource limitation is formulated based on the product of several Monod functions. Our study has created a new avenue for phytoplankton coexistence research and the results might be helpful to answer the complex questions on species diversity maintenance in nature.