The use of lake macrophytes for ecological quality assessments usually seeks to indicate the degree of anthropogenic impact, but few of these schemes implicitly consider impacts of alien weeds. LakeSPI (submerged plant indicators) uses indicators of habitat degradation for macrophytes but also incorporates the degree of impact from alien weeds. Application of LakeSPI to 195 New Zealand lakes provided a dataset to examine how component metrics responded over gradients of anthropogenic pressures, and consider whether weed invasion was merely a ‘passenger’ of habitat degradation, or represented an additional pressure. As expected, metrics measuring depth, and diversity of native vegetation negatively correlated with independent measures of lake eutrophy and were also relatively well explained (69–78% variation) by multiple regression with lake and catchment attributes that included proxies for anthropogenic pressure. In contrast, metrics for invasive impact were largely de-coupled from eutrophication, and poorly explained (31%) by the multiple regression. The response of native vegetation metrics to invasive impact measures varied, with the strongest detected interaction relating to native displacement by increased weed occupation of the vegetated zone. Interactions between invasion and lake trophic status were also discerned, with the extent of weed occupation having a more substantial outcome for the presence of charophyte meadows in low productivity lakes than in more productive lakes. These results suggest weed invasion should be considered as an additional source of anthropogenic pressure, and incorporated in macrophyte bioassessment schemes for a more complete differentiation of lake ecological condition.