This data contains fatty acid and amino acid contents and relative proportions of littoral and pelagic invertebrates in 8-9 subarctic lakes in Finnish Lapland. There are 23 littoral macroinvertebrate taxa measured, as well as two zooplankton taxa. There are also water quality parameters and geographic information about the studied lakes. Invertebrates were sampled for the fatty acid and amino acids between 15th - 25th August in 2017. Water quality samples were collected 2009-2013. Samples were collected with kick-net sampling or by vertical net tows. More detailed sampling methods and analyses are described in doi: 10.1002/lno.11563.