Most studies of phytoplankton dynamics in lowland rivers have been conducted in regulated rivers. This study deals the phytoplankton of the River Loire, a relatively unregulated river in Western Europe, and aims at investigating the factors controlling phytoplankton composition and dynamics in this river. Phytoplankton biodiversity was assessed by pooling data from monthly sampling for 8 years at different sites. A correspondence analysis showed temporal and longitudinal gradients, with a dominance of small centric diatoms and green algae for most of the year, in the middle and lower river sectors. Phytoplankton dynamics were further explored using the POTAMON simulation model, run for the year 2005. The simulations, in agreement with the observations, confirmed the virtual absence of a Stephanodiscus spring peak, and reproduced well the development of small centric diatoms and green algae. Production and loss rates calculated by the model helped us to explain the dynamics of the three main phytoplankton categories, which attained high net production rates due to the low river depth (∼1 m at low discharge), but were subject to high sedimentation losses. Model calculations also showed that P limitation was likely, particularly for green algae, with a reduction of growth rate of up to 35. In addition, the simulations showed a significant impact of the invasive Asian clam, Corbicula spp., on phytoplankton biomass. This study shows that the factors determining phytoplankton diversity and dynamics in this unregulated river are basically the same as those identified in other lowland rivers, but that key factors are habitat diversity and variation of water level in the river channel.