This dataset is part of a study investigating the freshwater Nitrososphaeria and their impact on the nitrogen cycling in lakes. It includes monthly measurements of nitrate and ammonia concentrations in the whole water column (1-135 m) in Lake Constance (Germany) from November 2017 to November 2019. Water was taken with a Niskin bottle and pre-filtered on board directly through 0.2µm. The indicated time represents the sampling time.