We investigated the microbial nitrogen cycle in the water column of the meromictic Lake Lugano North Basin, Switzerland, during 12 sampling campaigns between 2015 and 2018. At the deepest point of the lake, we sampled water between 75 and 165 m depth using Niskin bottles, and analyzed concentrations of N, S, and Fe species as well as isotope characteristics of nitrate. The dataset also contains whole water column profiles of physicochemical parameters measured with a conductivity, temperature, depth probe. In incubation experiments with 15N-labelled nitrate, without or with additional sulfide or acetate, we determined rates of denitrification, anammox, and dissimilatory nitrate reduction to ammonium to study nitrogen removal versus nitrogen recycling processes. In addition, we performed incubation experiments with added nitrate (and additional sulfide or acetate) using water samples from Lake Lugano as well as from the meromictic Lake La Cruz, Spain, to determine the N and O isotope effects of nitrate reduction in natural lake water consortia.