The effects of nutrient effluents from fish cage aquaculture are an important eutrophication concern. It has been proposed that marine fish farm derived nutrients have the potential to increase phytoplankton abundance and lead to intensification of Harmful Algal Blooms (HABs), and that these blooms may negatively impact both the finfish and the shellfish industry. This study addressed this hypothesis using farmed salmon biomass in Scottish marine waters (as a proxy for nutrient load added to the water column as a consequence of fish farming) cell abundance of HAB taxa that most frequently impact shellfish farms and human health in the region (Dinophysis spp., Alexandrium spp. and Pseudo-nitzschia spp.), and cell abundance of one phytoplankton species of particular concern to the salmon farming industry (Karenia mikimotoi). Data from a 15-year weekly HAB monitoring programme and parallel national monitoring data relating to salmon farm stocking biomass were summarised in 5 km per 5 km aggregation boxes. Linear regression models were used to assess (i) inter-annual variation in cell abundance and total annual farmed salmon biomass; (ii) intra-annual (monthly) variation in harmful phytoplankton cell abundance and salmon biomass; (iii) a further analysis included seasonal effects within the intra-annual analysis. Farmed salmon biomass alone had a non-significant effect on cell abundance of any of the studied phytoplankton taxa. In contrast, a significant effect on cell abundance was found when using location, month or season as the predictive variable. Despite the non-significant impact of fish biomass on phytoplankton counts, the relationship varied seasonally, with a different response of Dinophysis spp. indicating a taxa specific interaction. A possible explanation for the lack of a significant relationship between farmed salmon and harmful phytoplankton cell abundance is that aquaculture farms are generally located in hydrodynamically energetic locations where recurrent flushing likely allows efficient dilution of nutrients. Overall, the analyses suggest that current levels of salmon farming activities do not markedly impact the abundance of routinely monitored biotoxin producing or fish killing phytoplankton taxa in Scottish waters.