Environmental change can have a significant impact on biogeochemical cycles at high latitudes and be particularly important in ecologically valuable fjord ecosystems. Seasonality in biogeochemical cycling in a sub-Arctic fjord of northern Norway (Kaldfjorden) was investigated from October 2016 to September 2018. Monthly changes in total inorganic carbon (CT), alkalinity (AT), major nutrients and calcium carbonate saturation (Ω) were driven by freshwater discharge, biological production and mixing with subsurface carbon-rich coastal water. Stable oxygen isotope ratios indicated that meteoric water (snow melt, river runoff, precipitation) had stratified and freshened surface waters, contributing to 81% of the monthly CT deficit in the surface layer. The timing and magnitude of freshwater inputs played an important role in Ω variability, reducing AT and CT by dilution. This dilution effect was strongly counteracted by the opposing effect of primary production that dominated surface water Ω seasonality. The spring phytoplankton bloom rapidly depleted nitrate and CT to drive highest Ω (~2.3) in surface waters. Calcification reduced AT and CT, which accounted for 21% of the monthly decrease in Ω during a coccolithophore bloom. Freshwater runoff contributed CT, AT and silicates of terrestrial origin to the fjord. Lowest surface water Ω (~1.6) resulted from organic matter remineralisation and mixing into subsurface water during winter and spring. Surface waters were undersaturated with respect to atmospheric CO2, resulting in modest uptake of –0.32 ± 0.03 mol C m–2 yr–1. Net community production estimated from carbon drawdown was 14 ± 2 g C m–2 yr–1 during the productive season. Kaldfjorden currently functions as an atmospheric CO2 sink of 3.9 ± 0.3 g C m–2 yr–1. Time-series data are vital to better understand the processes and natural variability affecting biogeochemical cycling in dynamic coastal regions and thus better predict the impact of future changes on important fjord ecosystems.