The Fram Strait is the main gateway for water, heat and sea-ice exchanges between the Arctic Ocean and the North Atlantic. The complex physical environment results in a highly variable primary production in space and time. Previous regional studies have defined key bottom-up (ice cover and stratification from melt water controlling the light availability, and wind mixing and water transport affecting the supply of nutrients) and top-down processes (heterotrophic grazing). In this study, in situ field data, remote sensing and modeling techniques were combined to investigate in detail the influence of melting sea-ice and ocean properties on the development of phytoplankton blooms in the Fram Strait region for the years 1998–2009. Satellite-retrieved chlorophyll-a concentrations from temporarily ice-free zones were validated with contextual field data. These were then integrated per month on a grid size of 20 × 20 km, resulting in 10 grids/fields. Factors tested for their influence on spatial and temporal variation of chlorophyll-a were: sea-ice concentration from satellite and sea-ice thickness, ocean stratification, water temperature and salinity time-series simulated by the ice-ocean model NAOSIM. The time series analysis for those ten ice-free fields showed a regional separation according to different physical processes affecting phytoplankton distribution. At the marginal ice zone the melting sea-ice was promoting phytoplankton growth by stratifying the water column and potentially seeding phytoplankton communities. In this zone, the highest mean chlorophyll concentration averaged for the productive season (April–August) of 0.8 mgC/m3 was observed. In the open ocean the phytoplankton variability was correlated highest to stratification formed by solar heating of the upper ocean layers. Coastal zone around Svalbard showed processes associated with the presence of coastal ice were rather suppressing than promoting the phytoplankton growth. During the twelve years of observations, chlorophyll concentrations significantly increased in the southern part of the Fram Strait, associated with an increase in sea surface temperature and a decrease in Svalbard coastal ice.