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Abstract Inorganic nutrients can vary over space and time in lakes due to abiotic and biotic factors. To understand the drivers of spatial variation in nutrients in shallow Lake Mývatn, Iceland, we mapped dissolved inorganic and organic nitrogen (N) and phosphorus (P) concentrations in benthic (interstitial) and pelagic zones in summer 2021 during a lake-wide pelagic cyanobacterial bloom and in spring 2022 when there was no cyanobacterial bloom. We expected the bloom to affect nutrient distributions between zones through shading and N 2 fixation. Nutrient concentrations were neither correlated between the benthic and pelagic zone nor correlated between sampling events. The low ratio of total dissolved N to P implied that the benthos was N-limited, while the pelagic zone switched from N to P limitation during the summer cyanobacterial bloom. Interstitial ammonium concentrations were higher in summer than spring sampling events, positively associated with depth, and negatively associated with epipelic diatom density, associations that were stronger in spring. In summer, pelagic phosphate was highest near the springs; this pattern was reversed in the spring sampling event, although the effect size was weak. Variation in interstitial phosphate was not strongly associated with any of our predictors. Pelagic ammonium, and both interstitial and pelagic nitrate, were near or below detection limits. Together, these results highlight the capacity for large spatiotemporal variation in dissolved inorganic and organic N and P concentrations and nutrient limitation which will impact the structure and function of the Mývatn ecosystem.