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Abstract To evaluate effects of habitat modification at different spatial scales, we assessed species richness and tolerance of fish assemblages in littoral zones of 17 Wisconsin lakes with extensive residential and recreational development, and compared fish associations among site‐specific and lakewide conditions. Samples consisted of combined DC electrofishing and seining. Stations were randomly selected within strata defined by type of shoreline erosion control structure, including retaining walls, rock riprap, and no structure. Habitat characteristics differed among the site types. Species richness at the site level was greatest in complex habitat (riprap) regardless of fish assemblage structure. However, more effort was required to achieve complete sampling of fish species present in sites without erosion control structures. This result may be related to homogeneity of habitat among sites altered by manmade structures. We used an analysis of covariance (ANCOVA) to compare site level habitat effects with basin scale impacts as indexed by total phosphorus, which is affected by land use in the riparian zone and surrounding watershed. Although species richness is positively correlated with local habitat complexity across the range of lakes sampled, assemblage structure, assessed as proportion of intolerant or tolerant species, shifted in response to cumulative effects. Habitat management programs, such as shore land zoning and permitting, should consider the cumulative effects of small habitat modifications in addition to local effects.