The Department of Agriculture and Natural Resources maintains an extensive surface water quality monitoring network at many of South Dakota's streams. There are currently 154 active ambient monitoring stations across the state. The data from these sampling stations helps the Department identify problems, document improvements and demonstrate overall trends in the quality of South Dakota waters.
https://danr.sd.gov/OfficeOfWater/WaterRights/default.aspx
Lake level data
https://apps.sd.gov/NR65LakeInfo/public.aspx
Observation wells
https://apps.sd.gov/NR69obswell/default.aspx
Streamgage data I'm not sure where the shapefile or data are. They seem to be sharing data for a bunch of stations through NOAA Weather Service
https://sdbit.maps.arcgis.com/apps/Cascade/index.html?appid=284ac20e2a0e4e82b4584c383f3ed7b1
Lake level data
https://apps.sd.gov/NR65LakeInfo/public.aspx
Observation wells
https://apps.sd.gov/NR69obswell/default.aspx
Streamgage data I'm not sure where the shapefile or data are. They seem to be sharing data for a bunch of stations through NOAA Weather Service
https://sdbit.maps.arcgis.com/apps/Cascade/index.html?appid=284ac20e2a0e4e82b4584c383f3ed7b1