Seasonal and interannual (2002–2019) variations in the abundance (ind. m^-2) and population structure of the glacial relict amphipod Monoporeia affinis in a small subarctic Lake Krivoe (North-West of the Russian Federation) are presented. The study site (66⁰ 20.774′ N and 33⁰ 37.77′ E) was situated in the sublittoral zone at the depth of 8.5 m. Materials were collected from June 2002 to December 2019 mainly during the ice-free period (late May – October) as a rule, 4–5 times a season. 
In addition, the next data sets used in interpretation of population dynamics are presented:
(1) Changes in mean near- bottom (7–8 m) temperature (± range) and mean chlorophyll a (0–7 m) concentration (µg l^-1) gat study site during open-water period (May – October) in 2002–2019.
(2) Changes in mean annual abundance (ind. m^-2) of main macrobenthic taxa at study site in 2002–2019.

Materials were collected at one site (depth 8.5 m) from 2002 to 2019 mainly during the ice-free period (late May – October) as a rule, 4–5 times a season. Benthic samples were taken by standard Van-Veen grab (area 0.025 m²) in five replicates and were sieved through a screen with mesh sizes of 0.25 mm. In the laboratory, all macroinvertebrates were sorted and preserved in 70% ethanol. To estimate the age structure of Monoporeia affinis population, the body length (distance between rostrum and telson base) of preserved amphipods was later measured to the nearest 0.1 mm. Altogether about 4 000 (that is 50 individuals per sampling occasion) amphipods were measured. The age groups were separated subjectively based on histograms of length-frequency distribution.
Near-bottom (7–8 m) temperature during the ice-free period was measured on a biweekly or monthly basis. The mean temperature was calculated by integrating these data. The concentration of chlorophyll from 2010 was obtained from monthly integral water column samples (0–7m) collected by Ruttner bottle from May to October. The earlier (2002–2009) data are average annual values accepted from Maximov et al. (2021). In both cases, the concentration of chlorophyll a was measured using standard technique (UNESCO 1966). The mean concentration (±standard error) of concentration chlorophyll a was calculated by pooling water samples taken at study site during open-water period. Earlier published data of 2002–2009 are presented without standard errors because seasonal data series are not available.

The readme file contains an explanation of each of the variables in the dataset, its measurement units.