The EU Water Framework Directive is a Community legislative instrument in the field of environmental protection that establishes a common framework for keeping water quality at a favourable level. To implement the directive, classification systems need to be established that allow detection of human impacts at early stages and, thus, more effective management of coastal communities. Due to the spatial variability of communities, however, the results of any assessment are highly dependent on the selection of data. In this study we identified local spatial scales in which variability of macrophyte communities was maximised, quantified links between observed patterns of sediment types and communities and estimated how selection criteria impacted the outcome of the assessment of indicator class value in four different communities of the Northern Baltic Sea. The main findings of the study were that: (i) there were no clear local spatial scales in which the variability of benthic communities was maximised; (ii) hard-bottom communities were better predicted by the spatial arrangement of sediment characteristics than soft-bottom communities; (iii) the selection of method had no effect on the estimates of macrophyte cover and indicator class; but (iv) method impacted independently of habitat type on error estimates of macrophyte cover and indicator class. To conclude, in such homogeneous and low diversity macrophyte communities it is preferable to use methods that result in lower error estimates of algal coverage and, thus, result in lower uncertainties of estimates in the water quality class.