Lowrance SL2 files (saved as csv) and Garmin GPX files both save "Altitude" data in the datasets. When you are chugging around on a lake, mapping or fishing away peacefully, in theory your altitude should remain pretty constant.
GPS gives position data in 3 dimensions, and while positional innaccuracy is not obvious when just looking at latitude and longitude, a wildly varying altitude is a very good indicator that something is wrong and that your GPS 2d position data is likely to contain errors.
Neither of the two datasets (Lowrance or Garmin) store DOP (dilution of precision) information, so it is almost impossible to analyse the data afterwards to find areas where the positional accuracy was out.
The graph above is a DOP graph for a 3 hour period in August when I was surveying a small lake. The blue line is from an excel chart of altitude vs time.
On the right the top table is a section of a gpx file during the period of good DOP.