Water (physico)chemical and sediment chemical data from shallow tropical lakes and some piscicultures are available. In 5 subsequent field campaigns in both dry (3x) and rainy (2x) seasons from September 2021 to August 2023, we targeted five lake basins, including a large reservoir (Balbina), and 2 pisciculture sites in Amazonas state, Brazil. The lakes are Caldeirao and Jandira (blackwater), and Grande and Iranduba (whitewater), all on Iranduba peninsula to the WSW of Manaus. The two piscicultural sites are near the town of Rio Preto da Eva, NE from Manaus, and comprise various basins each with site 1 being used for raising young fish and site 2 for the production of edible fish.Water samples from different depth were taken repetitively with a contamination-free sampler. These samples were treated onboard (membrane filtration, acidification for cations, cooling) and stored in ultrapure acid-cleaned HDPE containers; the membrane filters for the water samples were kept and later analyzed for carbon, nitrogen and sulphur (by elemental analysis, El Cube from Elementar).