This dataset contains measurements of water (chemistry and algal pigments) and sediment (chemistry and size fraction) quality in nearshore areas of Lake Huron surrounding cage aquaculture operations including North Channel, Manitoulin Island and Georgian Bay. Seasonal ice-free monitoring and sampling occurred in Ontario nearshore areas between 1998-2016. The dataset also contains the limits of detection and quantification for the parameters measured, GPS coordinates and depths (sample, Secchi, composite and maximum) for the lake sampling locations.