Hornsund and Kongsfjorden are two similar-sized Arctic fjords on the West coast of Spitsbergen. They are influenced by cold coastal Arctic water (Hornsund) and warmer Atlantic water (Kongsfjorden). Environmental conditions affect the timing, quantity, spatial distribution (horizontal and vertical) of spring and summer blooms of protists as well as the taxonomic composition of those assemblages. Here, we compile published data and unpublished own measurement from the past two decades to compare the environmental factors and primary production in two fjord systems. Kongsfjorden is characterized by a deeper euphotic zone, higher biomass and greater proportion of autotrophic species. Hornsund seems to obtain more nutrients due to the extensive seabird colonies and exhibits higher turbidity compared to Kongsfjorden. The annual primary production in the analysed fjords ranges from 48 g C m-2 y-1 in Kongsfjorden to 216 g C m-2 y-1 in Hornsund, with a dominant component of microplankton (90%) followed by macrophytes and microphytobenthos.