Selected shorelines and offshore shoals in Lakes Erie, Huron and Ontario were surveyed with a high frequency hydroacoustic system to investigate current spatial patterns of nuisance benthic filamentous algal (e.g., Cladophora) cover and stand height. Cladophora reached nuisance levels at all sites in Lakes Erie and Ontario, but not in Lake Huron or Georgian Bay. Despite clear gradients in coastal land cover, near shore water quality gradients were generally weak, and for Lakes Erie and Ontario, measures of near shore water quality were similar to that at offshore shoals. Hierarchical partitioning analysis suggested that while dreissenid mussel abundance appeared to be important in determining the magnitude of Cladophora standing crop, the joint contribution of catchment land cover, near shore water quality (nutrient levels and suspended matter) and dreissenid mussel abundance explained nearly 95% of the total variance in nuisance Cladophora standing crop observed in this study. Although the results from this study are necessarily correlative in nature and definition of causal relationships is not possible, these results provide corroborating evidence from sites across a gradient within and across the lower Great Lakes that is consistent with the operation of the near shore shunt model. (C) 2011 International Association for Great lakes Research. Published by Elsevier B.V. All rights reserved.